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annotate mqppep_anova_script.Rmd @ 15:2c5f1a2fe16a draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
author eschen42
date Sat, 26 Mar 2022 02:27:12 +0000
parents 6679616d0c18
children 61adb8801b73
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1 ---
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2 title: "MaxQuant Phospho-Proteomic Enrichment Pipeline ANOVA"
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3 author: "Larry Cheng; Art Eschenlauer"
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4 date: "May 28, 2018; Mar 16, 2022"
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5 output:
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6 pdf_document:
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7 toc: true
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8 latex_document:
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9 toc: true
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10 params:
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11 alphaFile: "test-data/alpha_levels.tabular"
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12 inputFile: "test-data/UT_Phospho_ST_Sites.preproc.tabular"
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13 firstDataColumn: "^Intensity[^_]"
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14 imputationMethod: !r c("group-median", "median", "mean", "random")[4]
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15 meanPercentile: 1
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16 sdPercentile: 1.0
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17 regexSampleNames: "\\.\\d+[A-Z]$"
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18 regexSampleGrouping: "\\d+"
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19 imputedDataFilename: "test-data/limbo/imputedDataFilename.txt"
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20 imputedQNLTDataFile: "test-data/limbo/imputedQNLTDataFile.txt"
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21 show_toc: true
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22 ---
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23 <!--
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24 alphaFile: "test-data/alpha_levels.tabular"
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25 inputFile: "test-data/test_input_for_anova.tabular"
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26 inputFile: "test-data/UT_Phospho_ST_Sites.preproc.tabular"
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27 inputFile: "test-data/density_failure.preproc_tab.tabular"
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28 latex_document: default
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29 -->
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30 ```{r setup, include = FALSE}
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31 # ref for parameterizing Rmd document: https://stackoverflow.com/a/37940285
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32 knitr::opts_chunk$set(echo = FALSE, fig.dim = c(9, 10))
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33
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34 # freeze the random number generator so the same results will be produced
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35 # from run to run
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36 set.seed(28571)
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38 ### CONSTANTS
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40 const_parfin <- par("fin")
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41 const_boxplot_fill <- "grey94"
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42 const_stripchart_cex <- 0.5
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43 const_stripsmall_cex <-
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44 sqrt(const_stripchart_cex * const_stripchart_cex / 2)
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45 const_stripchart_jitter <- 0.3
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46 const_write_debug_files <- FALSE
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47 const_table_anchor <- "tbp"
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48
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49 ### FUNCTIONS
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51 #ANOVA filter function
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52 anova_func <- function(x, grouping_factor) {
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53 x_aov <- aov(as.numeric(x) ~ grouping_factor)
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54 pvalue <- summary(x_aov)[[1]][["Pr(>F)"]][1]
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55 pvalue
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56 }
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57
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58 write_debug_file <- function(s) {
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59 if (const_write_debug_files) {
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60 s_path <- sprintf("test-data/%s.txt", deparse(substitute(s)))
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61 write.table(
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62 s,
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63 file = s_path,
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64 sep = "\t",
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65 col.names = TRUE,
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66 row.names = TRUE,
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67 quote = FALSE
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68 )
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69 }
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70 }
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71
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72 latex_collapsed_vector <- function(collapse_string, v) {
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73 cat(
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74 paste0(
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75 gsub("_", "\\\\_", v),
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76 collapse = collapse_string
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77 )
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78 )
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79 }
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80
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81 latex_itemized_collapsed <- function(collapse_string, v) {
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82 cat("\\begin{itemize}\n\\item ")
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83 latex_collapsed_vector(collapse_string, v)
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84 cat("\n\\end{itemize}\n")
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85 }
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diff changeset
86
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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87 latex_itemized_list <- function(v) {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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88 latex_itemized_collapsed("\n\\item ", v)
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89 }
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
90
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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91 latex_enumerated_collapsed <- function(collapse_string, v) {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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92 cat("\\begin{enumerate}\n\\item ")
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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93 latex_collapsed_vector(collapse_string, v)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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94 cat("\n\\end{enumerate}\n")
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
95 }
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
96
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
97 latex_enumerated_list <- function(v) {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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98 latex_enumerated_collapsed("\n\\item ", v)
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diff changeset
99 }
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
100
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
101 latex_table_row <- function(v) {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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102 latex_collapsed_vector(" & ", v)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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103 cat(" \\\\\n")
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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104 }
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
105
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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106 # Use this like print.data.frame, from which it is adapted:
15
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107 data_frame_latex <-
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
108 function(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
109 x,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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110 ...,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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111 # digits to pass to format.data.frame
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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112 digits = NULL,
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113 # TRUE -> right-justify columns; FALSE -> left-justify
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114 right = TRUE,
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115 # maximumn number of rows to print
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116 max = NULL,
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117 # string with justification of each column
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118 justification = NULL,
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119 # TRUE to center on page
15
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120 centered = TRUE,
13
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121 # optional capttion
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122 caption = NULL,
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123 # h(inline); b(bottom); t (top) or p (separate page)
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124 anchor = "h"
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125 ) {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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126 if (is.null(justification))
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127 justification <-
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128 Reduce(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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129 f = paste,
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130 x = rep_len(if (right) "r" else "l", length(colnames(x)))
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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131 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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132 n <- length(rownames(x))
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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133 if (length(x) == 0L) {
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134 cat(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
135 sprintf(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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136 # if n is one, use singular 'row', else use plural 'rows'
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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137 ngettext(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
138 n,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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139 "data frame with 0 columns and %d row",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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140 "data frame with 0 columns and %d rows"
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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141 ),
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
142 n
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
143 ),
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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144 "\n",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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145 sep = ""
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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146 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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147 }
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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148 else if (n == 0L) {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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149 cat("0 rows for:\n")
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150 latex_itemized_list(names(x))
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
151 }
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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152 else {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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153 if (is.null(max))
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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154 max <- getOption("max.print", 99999L)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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155 if (!is.finite(max))
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
156 stop("invalid 'max' / getOption(\"max.print\"): ",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
157 max)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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158 omit <- (n0 <- max %/% length(x)) < n
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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159 m <- as.matrix(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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160 format.data.frame(
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diff changeset
161 if (omit) x[seq_len(n0), , drop = FALSE] else x,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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162 digits = digits,
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163 na.encode = FALSE
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diff changeset
164 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
165 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
166 cat(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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167 # h(inline); b(bottom); t (top) or p (separate page)
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diff changeset
168 paste0("\\begin{table}[", anchor, "]\n")
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
169 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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170 if (!is.null(caption))
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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171 cat(paste0(" \\caption{", caption, "}"))
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172 if (centered) cat("\\centering\n")
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173 cat(
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174 paste(
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175 " \\begin{tabular}{",
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176 justification,
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177 "}\n",
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178 sep = ""
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179 )
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180 )
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181 if (!is.null(caption))
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182 cat(" \\hline\\hline\n")
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183 latex_table_row(colnames(m))
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184 cat("\\hline\n")
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185 for (i in seq_len(length(m[, 1]))) {
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186 latex_table_row(m[i, ])
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187 }
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188 cat(
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189 paste(
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190 " \\end{tabular}",
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191 "\\end{table}",
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192 sep = "\n"
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193 )
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194 )
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195 if (omit)
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196 cat(" [ reached 'max' / getOption(\"max.print\") -- omitted",
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197 n - n0, "rows ]\n")
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198 }
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199 invisible(x)
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200 }
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201
0
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202 ```
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203
15
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204 ## Purpose
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205
0
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206 Perform imputation of missing values, quantile normalization, and ANOVA.
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207
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208 ```{r include = FALSE}
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209 # Input Filename
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210 input_file <- params$inputFile
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211
7
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212 # First data column - ideally, this could be detected via regexSampleNames,
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213 # but for now leave it as is.
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214 first_data_column <- params$firstDataColumn
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215 fdc_is_integer <- is.integer(first_data_column)
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216 if (fdc_is_integer) {
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217 first_data_column <- as.integer(params$firstDataColumn)
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218 }
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219
7
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220 # False discovery rate adjustment for ANOVA
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221 # Since pY abundance is low, set to 0.10 and 0.20 in addition to 0.05
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222 val_fdr <-
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223 read.table(file = params$alphaFile, sep = "\t", header = F, quote = "")
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224
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225 if (
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226 ncol(val_fdr) != 1 ||
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227 sum(!is.numeric(val_fdr[, 1])) ||
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228 sum(val_fdr[, 1] < 0) ||
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229 sum(val_fdr[, 1] > 1)
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230 ) {
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231 stop("alphaFile should be one column of numbers within the range [0.0,1.0]")
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232 }
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233 val_fdr <- val_fdr[, 1]
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234
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235 #Imputed Data filename
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236 imputed_data_filename <- params$imputedDataFilename
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237 imp_qn_lt_data_filenm <- params$imputedQNLTDataFile
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238
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239 #ANOVA data filename
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240 ```
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241
7
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242 ```{r echo = FALSE}
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243 # Imputation method, should be one of
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244 # "random", "group-median", "median", or "mean"
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245 imputation_method <- params$imputationMethod
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246
7
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247 # Selection of percentile of logvalue data to set the mean for random number
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248 # generation when using random imputation
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249 mean_percentile <- params$meanPercentile / 100.0
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250
7
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251 # deviation adjustment-factor for random values; real number.
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252 sd_percentile <- params$sdPercentile
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253
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254 # Regular expression of Sample Names, e.g., "\\.(\\d+)[A-Z]$"
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255 regex_sample_names <- params$regexSampleNames
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256
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257 # Regular expression to extract Sample Grouping from Sample Name;
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258 # if error occurs, compare sample_factor_levels and sample_name_matches
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259 # to see if groupings/pairs line up
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260 # e.g., "(\\d+)"
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261 regex_sample_grouping <- params$regexSampleGrouping
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262
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263 ```
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264
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265 ```{r echo = FALSE}
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266 ### READ DATA
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267
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268 library(data.table)
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269
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270 # read.table reads a file in table format and creates a data frame from it.
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271 # - note that `quote = ""` means that quotation marks are treated literally.
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272 full_data <- read.table(
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273 file = input_file,
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274 sep = "\t",
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275 header = T,
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276 quote = "",
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277 check.names = FALSE
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278 )
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279 ```
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280
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281 ## Extract Sample Names and Factor Levels
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282
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283 Column names parsed from input file are shown in Table 1; sample names and factor levels, in Table 2.
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284
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285 ```{r echo = FALSE, results = 'asis'}
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286
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287 data_column_indices <- grep(first_data_column, names(full_data), perl = TRUE)
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288
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289 if (!fdc_is_integer) {
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290 if (length(data_column_indices) > 0) {
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291 first_data_column <- data_column_indices[1]
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292 } else {
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293 stop(paste("failed to convert firstDataColumn:", first_data_column))
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294 }
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295 }
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296
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297 cat(
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298 sprintf(
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299 paste(
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300 "\n\nPeptide-intensity data for each sample is",
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301 "in one of columns %d through %d.\n\n"
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302 ),
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303 min(data_column_indices),
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304 max(data_column_indices)
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305 )
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306 )
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307
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308 # Write column names as a LaTeX enumerated list.
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309 column_name_df <- data.frame(
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310 column = seq_len(length(colnames(full_data))),
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311 name = colnames(full_data)
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312 )
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313 data_frame_latex(
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314 x = column_name_df,
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315 justification = "l l",
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316 centered = TRUE,
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317 caption = "Input data column name",
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318 anchor = const_table_anchor
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319 )
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320
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321 ```
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322
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323 ```{r echo = FALSE, results = 'asis'}
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324 #```{r echo = FALSE, results = 'asis'}
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325 quant_data <- full_data[first_data_column:length(full_data)]
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326 quant_data[quant_data == 0] <- NA
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327 rownames(quant_data) <- full_data$Phosphopeptide
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328 # Get factors -> group replicates (as indicated by terminal letter)
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329 # by the preceding digits;
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330 # Assuming that regex_sample_names <- "\\.(\\d+)[A-Z]$"
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331 # get factors ->
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332 # group runs (samples) by ignoring terminal [A-Z] in sample names
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333 # e.g.
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334 # group .1A .1B .1C into group 1;
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335 # group .2A .2B .2C, into group 2;
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336 # etc.
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337 m <- regexpr(regex_sample_names, colnames(quant_data), perl = TRUE)
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338 sample_name_matches <- regmatches(names(quant_data), m)
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339 colnames(quant_data) <- sample_name_matches
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340
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341 write_debug_file(quant_data)
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342
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343 m2 <- regexpr(regex_sample_grouping, sample_name_matches, perl = TRUE)
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344 sample_factor_levels <- as.factor(regmatches(sample_name_matches, m2))
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345 number_of_samples <- length(sample_name_matches)
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346 sample_factor_df <- data.frame(
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347 sample = sample_name_matches,
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348 level = sample_factor_levels
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349 )
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350 data_frame_latex(
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351 x = sample_factor_df,
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352 justification = "c c",
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353 centered = TRUE,
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354 caption = "Factor level",
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355 anchor = const_table_anchor
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356 )
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357 ```
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358 ```{r echo = FALSE, results = 'asis'}
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359 cat("\\newpage\n")
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360 ```
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361
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362 ### Are the log-transformed sample distributions similar?
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363
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364 ```{r echo = FALSE, fig.dim = c(9, 5.5), results = 'asis'}
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365
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366 quant_data[quant_data == 0] <- NA #replace 0 with NA
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367 quant_data_log <- log10(quant_data)
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368
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369 rownames(quant_data_log) <- rownames(quant_data)
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370 colnames(quant_data_log) <- sample_name_matches
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371
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372 write_debug_file(quant_data_log)
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373
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374 # data visualization
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375 old_par <- par(
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376 mai = par("mai") + c(0.5, 0, 0, 0)
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377 )
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378 # ref: https://r-charts.com/distribution/add-points-boxplot/
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379 # Vertical plot
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380 boxplot(
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381 quant_data_log
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382 , las = 1
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383 , col = const_boxplot_fill
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384 , ylab = latex2exp::TeX("$log_{10}$(peptide intensity)")
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385 , xlab = "Sample"
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386 )
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387 par(old_par)
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388
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389
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390
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391 cat("\n\n\n")
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392 cat("\n\n\n")
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393
0
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394 ```
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395
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396 ```{r echo = FALSE, fig.align = "left", fig.dim = c(9, 4), results = 'asis'}
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397 library(ggplot2)
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398 if (nrow(quant_data_log) > 1) {
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399 quant_data_log_stack <- stack(quant_data_log)
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400 ggplot(
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401 quant_data_log_stack,
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402 aes(x = values)
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403 ) + xlab(latex2exp::TeX("$log_{10}$(peptide intensity)")) +
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404 ylab("Probability density") +
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405 geom_density(
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406 aes(group = ind, colour = ind),
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407 na.rm = TRUE
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408 )
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409 } else {
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410 cat("No density plot because there are too few peptides.\n\n")
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411 }
0
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412 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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413
13
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414 ### Globally, are peptide intensities are approximately unimodal?
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415
7
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416 <!--
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417 # bquote could be used as an alternative to latex2exp::TeX below particularly
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418 # and when plotting math expressions generally, at the expense of mastering
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419 # another syntax, which hardly seems worthwhile when I need to use TeX
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420 # elsewhere; here's an introduction to bquote:
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421 # https://www.r-bloggers.com/2018/03/math-notation-for-r-plot-titles-expression-and-bquote/
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422 -->
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423 ```{r echo = FALSE, fig.align = "left", fig.dim = c(9, 5), results = 'asis'}
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424
7
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425 # identify the location of missing values
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426 fin <- is.finite(as.numeric(as.matrix(quant_data_log)))
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427
7
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428 logvalues <- as.numeric(as.matrix(quant_data_log))[fin]
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diff changeset
429 logvalues_density <- density(logvalues)
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
430 plot(
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2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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diff changeset
431 x = logvalues_density,
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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432 main = latex2exp::TeX(
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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433 "Smoothed estimated probability density vs. $log_{10}$(peptide intensity)"
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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diff changeset
434 ),
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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diff changeset
435 xlab = latex2exp::TeX("$log_{10}$(peptide intensity)"),
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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diff changeset
436 ylab = "Probability density"
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d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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437 )
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
438 hist(
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2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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diff changeset
439 x = as.numeric(as.matrix(quant_data_log)),
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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440 xlim = c(min(logvalues_density$x), max(logvalues_density$x)),
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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441 breaks = 100,
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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442 main = latex2exp::TeX("Frequency vs. $log_{10}$(peptide intensity)"),
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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diff changeset
443 xlab = latex2exp::TeX("$log_{10}$(peptide intensity)")
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
444 )
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
445 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
446
13
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447 ### Distribution of standard deviations of $log_{10}(\text{intensity})$, ignoring missing values:
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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448
13
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diff changeset
449 ```{r echo = FALSE, fig.align = "left", fig.dim = c(9, 5), results = 'asis'}
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d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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450 # determine quantile
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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451 q1 <- quantile(logvalues, probs = mean_percentile)[1]
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c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
452
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
453 # determine standard deviation of quantile to impute
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c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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454 sd_finite <- function(x) {
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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455 ok <- is.finite(x)
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b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
456 sd(x[ok])
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c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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457 }
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d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
458 # 1 = row of matrix (ie, phosphopeptide)
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
459 sds <- apply(quant_data_log, 1, sd_finite)
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b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
460 if (sum(!is.na(sds)) > 2) {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
461 plot(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
462 density(sds, na.rm = T)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
463 , main = "Smoothed estimated probability density vs. std. deviation"
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
464 , sub = "(probability estimation made with Gaussian smoothing)"
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diff changeset
465 , ylab = "Probability density"
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b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
466 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
467 } else {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
468 cat(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
469 "At least two non-missing values are required to plot",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
470 "probability density.\n\n"
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
471 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
472 }
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
473
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
474 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
475
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
476 ```{r echo = FALSE}
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
477 # Determine number of cells to impute
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
478 temp <- quant_data[is.na(quant_data)]
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c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
479
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
480 # Determine number of values to impute
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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481 number_to_impute <- length(temp)
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c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
482
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
483 # Determine percent of missing values
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
484 pct_missing_values <-
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
485 round(length(temp) / (length(logvalues) + length(temp)) * 100)
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d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
486 ```
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
487
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
488 ```{r echo = FALSE}
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
489
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
490 # prep for trt-median based imputation
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
491
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
492 ```
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b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
493 ## Impute Missing Values
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
494
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
495 ```{r echo = FALSE}
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
496
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
497 imp_smry_potential_before <- length(logvalues)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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498 imp_smry_missing_before <- number_to_impute
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
499 imp_smry_pct_missing <- pct_missing_values
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
500
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
501 ```
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
502
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
503 ```{r echo = FALSE}
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
504 #Determine number of cells to impute
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
505
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
506 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
507 ```{r echo = FALSE}
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
508
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
509 #Impute data
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
510 quant_data_imp <- quant_data
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
511
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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512 # Identify which values are missing and need to be imputed
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
513 ind <- which(is.na(quant_data_imp), arr.ind = TRUE)
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
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diff changeset
514
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
515 ```
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
516 ```{r echo = FALSE, results = 'asis'}
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
517
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
518 # Apply imputation
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
519 switch(
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
520 imputation_method
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
521 , "group-median" = {
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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parents: 12
diff changeset
522 imputation_method_description <-
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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parents: 12
diff changeset
523 paste("Substitute missing value with",
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
524 "median peptide intensity for sample group.\n"
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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parents: 12
diff changeset
525 )
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
526 sample_level_integers <- as.integer(sample_factor_levels)
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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parents: 0
diff changeset
527 for (i in seq_len(length(levels(sample_factor_levels)))) {
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
528 level_cols <- i == sample_level_integers
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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parents: 0
diff changeset
529 ind <- which(is.na(quant_data_imp[, level_cols]), arr.ind = TRUE)
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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parents: 0
diff changeset
530 quant_data_imp[ind, level_cols] <-
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
531 apply(quant_data_imp[, level_cols], 1, median, na.rm = T)[ind[, 1]]
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
532 }
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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parents: 0
diff changeset
533 good_rows <- !is.na(rowMeans(quant_data_imp))
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
534 }
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
535 , "median" = {
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
536 imputation_method_description <-
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
537 paste("Substitute missing value with",
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
538 "median peptide intensity across all sample classes.\n"
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
539 )
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
540 quant_data_imp[ind] <- apply(quant_data_imp, 1, median, na.rm = T)[ind[, 1]]
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
541 good_rows <- !is.na(rowMeans(quant_data_imp))
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
542 }
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
543 , "mean" = {
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
544 imputation_method_description <-
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
545 paste("Substitute missing value with",
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
546 "mean peptide intensity across all sample classes.\n"
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
547 )
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
548 quant_data_imp[ind] <- apply(quant_data_imp, 1, mean, na.rm = T)[ind[, 1]]
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
549 good_rows <- !is.na(rowMeans(quant_data_imp))
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
550 }
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
551 , "random" = {
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
552 m1 <- median(sds, na.rm = T) * sd_percentile #sd to be used is the median sd
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
553 # If you want results to be reproducible, you will want to call
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
554 # base::set.seed before calling stats::rnorm
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
555 imputation_method_description <-
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
556 paste("Substitute each missing value with random intensity",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
557 sprintf(
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
558 "random intensity $N \\sim (%0.2f, %0.2f)$.\n",
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
559 q1, m1
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
560 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
561 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
562 cat(sprintf("mean_percentile (from input parameter) is %2.0f\n\n",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
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diff changeset
563 100 * mean_percentile))
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
564 cat(sprintf("sd_percentile (from input parameter) is %0.2f\n\n",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
565 sd_percentile))
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
566 quant_data_imp[ind] <-
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
567 10 ^ rnorm(number_to_impute, mean = q1, sd = m1)
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
568 good_rows <- !is.na(rowMeans(quant_data_imp))
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
569 }
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
570 )
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
571
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
572 if (length(good_rows) < 1) {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
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diff changeset
573 print("ERROR: Cannot impute data; there are no good rows!")
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
574 return(-1)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
575 }
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
576 ```
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
577
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
578 ```{r echo = FALSE, results = 'asis'}
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
579 cat("\\quad\n\nImputation method:\n\n\n", imputation_method_description)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
580 ```
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
581
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
582 ```{r echo = FALSE}
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
583
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
584 imp_smry_potential_after <- sum(good_rows)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
585 imp_smry_rejected_after <- sum(!good_rows)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
586 imp_smry_missing_after <- sum(is.na(quant_data_imp[good_rows, ]))
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
587 ```
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
588 ```{r echo = FALSE, results = 'asis'}
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
589 # ref: http://www1.maths.leeds.ac.uk/latex/TableHelp1.pdf
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
590 tabular_lines <- paste(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
591 "\\begin{table}[hb]", # h(inline); b(bottom); t (top) or p (separate page)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
592 " \\caption{Imputation Results}",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
593 " \\centering", # \centering centers the table on the page
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
594 " \\begin{tabular}{l c c c}",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
595 " \\hline\\hline",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
596 " \\ & potential peptides & missing values & rejected",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
597 " peptides \\\\ [0.5ex]",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
598 " \\hline",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
599 " before imputation & %d & %d (%d\\%s) & \\\\",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
600 " after imputation & %d & %d & %d \\\\ [1ex]",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
601 " \\hline",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
602 " \\end{tabular}",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
603 #" \\label{table:nonlin}", # may be used to refer this table in the text
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
604 "\\end{table}",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
605 sep = "\n"
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
606 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
607 tabular_lines <-
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
608 sprintf(
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
609 tabular_lines,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
610 imp_smry_potential_before,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
611 imp_smry_missing_before,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
612 imp_smry_pct_missing,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
613 "%",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
614 imp_smry_potential_after,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
615 imp_smry_missing_after,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
616 imp_smry_rejected_after
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
617 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
618 cat(tabular_lines)
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
619 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
620 ```{r echo = FALSE}
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
621
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
622
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
623 # Zap rows where imputation was ineffective
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
624 full_data <- full_data [good_rows, ]
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
625 quant_data <- quant_data [good_rows, ]
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
626
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
627 write_debug_file(quant_data_imp)
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
628
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
629 quant_data_imp <- quant_data_imp[good_rows, ]
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
630 quant_data_imp_good_rows <- quant_data_imp
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
631
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
632 write_debug_file(quant_data_imp_good_rows)
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
633 ```
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
634
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
635 ```{r echo = FALSE, results = 'asis'}
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
636
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
637 can_plot_before_after_imp <- TRUE
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
638 d_combined <-
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
639 as.numeric(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
640 as.matrix(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
641 log10(quant_data_imp)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
642 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
643 )
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
644 d_original <-
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
645 as.numeric(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
646 as.matrix(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
647 log10(quant_data_imp[!is.na(quant_data)])
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
648 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
649 )
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
650
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
651 if (sum(!is.na(d_combined)) > 2 && sum(!is.na(d_original)) > 2) {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
652 d_combined <- density(d_combined)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
653 d_original <- density(d_original)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
654 } else {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
655 can_plot_before_after_imp <- FALSE
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
656 }
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
657
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
658 if (sum(is.na(quant_data)) > 0) {
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
659 # There ARE missing values
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
660 d_imputed <-
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
661 as.numeric(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
662 as.matrix(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
663 log10(quant_data_imp[is.na(quant_data)])
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
664 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
665 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
666 if (sum(!is.na(d_combined)) > 2) {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
667 d_imputed <- (density(d_imputed))
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
668 } else {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
669 can_plot_before_after_imp <- FALSE
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
670 }
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
671 } else {
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
672 # There are NO missing values
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
673 d_imputed <- d_combined
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
674 }
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
675
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
676 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
677
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
678 ```{r echo = FALSE, fig.dim = c(9, 5.5), results = 'asis'}
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
679 if (sum(is.na(quant_data)) > 0) {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
680 cat("\\leavevmode\\newpage\n")
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
681 # data visualization
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
682 old_par <- par(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
683 mai = par("mai") + c(0.5, 0, 0, 0)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
684 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
685 x <- quant_data
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
686 x <- blue_dots <- x / x
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
687 blue_dots <- log10(blue_dots * quant_data)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
688 x[is.na(x)] <- 0
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
689 x[x == 1] <- NA
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
690 x[x == 0] <- 1
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
691 quant_data_imp_log10 <-
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
692 log10(quant_data_imp)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
693
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
694 write_debug_file(quant_data_imp_log10)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
695
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
696 red_dots <- quant_data_imp_log10 * x
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
697 count_red <- sum(!is.na(red_dots))
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
698 count_blue <- sum(!is.na(blue_dots))
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
699 ylim_save <- ylim <- c(
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
700 min(red_dots, blue_dots, na.rm = TRUE),
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
701 max(red_dots, blue_dots, na.rm = TRUE)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
702 )
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
703 show_stripchart <-
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
704 50 > (count_red + count_blue) / length(sample_name_matches)
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
705 if (show_stripchart) {
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
706 boxplot_sub <- "Light blue = data before imputation; Red = imputed data"
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
707 } else {
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
708 boxplot_sub <- ""
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
709 }
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
710
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
711 # Vertical plot
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
712 colnames(blue_dots) <- sample_name_matches
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
713 boxplot(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
714 blue_dots
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
715 , las = 1 # "always horizontal"
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
716 , col = const_boxplot_fill
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
717 , ylim = ylim
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
718 , main = "Peptide intensities before and after imputation"
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
719 , sub = boxplot_sub
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
720 , xlab = "Sample"
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
721 , ylab = latex2exp::TeX("$log_{10}$(peptide intensity)")
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
722 )
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
723
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
724 if (show_stripchart) {
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
725 # Points
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
726 # ref: https://r-charts.com/distribution/add-points-boxplot/
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
727 # NA values are not plotted
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
728 stripchart(
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
729 blue_dots, # Data
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
730 method = "jitter", # Random noise
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
731 jitter = const_stripchart_jitter,
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
732 pch = 19, # Pch symbols
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
733 cex = const_stripsmall_cex, # Size of symbols reduced
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
734 col = "lightblue", # Color of the symbol
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
735 vertical = TRUE, # Vertical mode
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
736 add = TRUE # Add it over
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
737 )
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
738 stripchart(
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
739 red_dots, # Data
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
740 method = "jitter", # Random noise
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
741 jitter = const_stripchart_jitter,
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
742 pch = 19, # Pch symbols
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
743 cex = const_stripsmall_cex, # Size of symbols reduced
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
744 col = "red", # Color of the symbol
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
745 vertical = TRUE, # Vertical mode
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
746 add = TRUE # Add it over
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
747 )
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
748
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
749 } else {
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
750 # violin plot
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
751 cat("\\leavevmode\n\\quad\n\n\\quad\n\n")
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
752 vioplot::vioplot(
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
753 x = lapply(blue_dots, function(x) x[!is.na(x)]),
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
754 col = "lightblue1",
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
755 side = "left",
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
756 plotCentre = "line",
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
757 ylim = ylim_save,
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
758 main = "Distributions of observed and imputed data",
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
759 sub = "Light blue = observed data; Pink = imputed data",
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
760 xlab = "Sample",
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
761 ylab = latex2exp::TeX("$log_{10}$(peptide intensity)")
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
762 )
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
763 vioplot::vioplot(
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
764 x = lapply(red_dots, function(x) x[!is.na(x)]),
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
765 col = "lightpink1",
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
766 side = "right",
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
767 plotCentre = "line",
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
768 add = T
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
769 )
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
770 }
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
771
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
772 par(old_par)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
773
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
774 # density plot
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
775 cat("\\leavevmode\n\n\n\n\n\n\n")
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
776 if (can_plot_before_after_imp) {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
777 ylim <- c(0, max(d_combined$y, d_original$y, d_imputed$y))
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
778 plot(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
779 d_combined,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
780 ylim = ylim,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
781 sub =
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
782 paste(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
783 "Blue = data before imputation; Red = imputed data;",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
784 "Black = combined"
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
785 ),
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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parents: 12
diff changeset
786 main = "Density of peptide intensity before and after imputation",
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
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parents: 14
diff changeset
787 xlab = latex2exp::TeX("$log_{10}$(peptide intensity)"),
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
788 ylab = "Probability density"
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
789 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
790 lines(d_original, col = "blue")
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
791 lines(d_imputed, col = "red")
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
792 } else {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
793 cat(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
794 "There are too few points to plot the density of peptide intensity",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
795 "before and after imputation."
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
796 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
797 }
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
798 cat("\\leavevmode\\newpage\n")
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
799 }
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
800 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
801
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
802 ## Perform Quantile Normalization
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
803
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
804 <!--
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
805 # Apply quantile normalization using preprocessCore::normalize.quantiles
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
806 # ---
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
807 # tool repository: http://bioconductor.org/packages/release/bioc/html/preprocessCore.html
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
808 # except this: https://support.bioconductor.org/p/122925/#9135989
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
809 # says to install it like this:
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
810 # ```
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
811 # BiocManager::install("preprocessCore", configure.args="--disable-threading", force = TRUE, lib=.libPaths()[1])
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
812 # ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
813 # conda installation (necessary because of a bug in recent openblas):
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
814 # conda install bioconductor-preprocesscore openblas=0.3.3
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
815 # ...
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
816 # ---
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
817 # normalize.quantiles {preprocessCore} -- Quantile Normalization
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
818 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
819 # Description:
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
820 # Using a normalization based upon quantiles, this function normalizes a matrix of probe level intensities.
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
821 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
822 # Usage:
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
823 # normalize.quantiles(x, copy = TRUE, keep.names = FALSE)
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
824 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
825 # Arguments:
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
826 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
827 # - x: A matrix of intensities where each column corresponds to a chip and each row is a probe.
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
828 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
829 # - copy: Make a copy of matrix before normalizing. Usually safer to work with a copy,
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
830 # but in certain situations not making a copy of the matrix, but instead normalizing
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
831 # it in place will be more memory friendly.
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
832 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
833 # - keep.names: Boolean option to preserve matrix row and column names in output.
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
834 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
835 # Details:
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
836 # This method is based upon the concept of a quantile-quantile plot extended to n dimensions.
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
837 # No special allowances are made for outliers. If you make use of quantile normalization
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
838 # please cite Bolstad et al, Bioinformatics (2003).
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
839 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
840 # This functions will handle missing data (ie NA values), based on
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
841 # the assumption that the data is missing at random.
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
842 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
843 # Note that the current implementation optimizes for better memory usage
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
844 # at the cost of some additional run-time.
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
845 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
846 # Value: A normalized matrix.
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
847 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
848 # Author: Ben Bolstad, bmbolstad.com
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
849 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
850 # References
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
851 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
852 # - Bolstad, B (2001) Probe Level Quantile Normalization of High Density Oligonucleotide
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
853 # Array Data. Unpublished manuscript http://bmbolstad.com/stuff/qnorm.pdf
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
854 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
855 # - Bolstad, B. M., Irizarry R. A., Astrand, M, and Speed, T. P. (2003) A Comparison of
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
856 # Normalization Methods for High Density Oligonucleotide Array Data Based on Bias
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
857 # and Variance. Bioinformatics 19(2), pp 185-193. DOI 10.1093/bioinformatics/19.2.185
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
858 # http://bmbolstad.com/misc/normalize/normalize.html
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
859 # ...
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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parents: 0
diff changeset
860 -->
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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parents: 12
diff changeset
861 ```{r echo = FALSE, results = 'asis'}
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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parents: 0
diff changeset
862 library(preprocessCore)
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
863
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
864 if (nrow(quant_data_imp) > 0) {
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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parents: 0
diff changeset
865 quant_data_imp_qn <- normalize.quantiles(as.matrix(quant_data_imp))
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
866 } else {
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
867 quant_data_imp_qn <- as.matrix(quant_data_imp)
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
868 }
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
869
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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parents: 0
diff changeset
870 quant_data_imp_qn <- as.data.frame(quant_data_imp_qn)
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
871 names(quant_data_imp_qn) <- names(quant_data_imp)
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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parents: 12
diff changeset
872
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
873 write_debug_file(quant_data_imp_qn)
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
874
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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diff changeset
875 quant_data_imp_qn_log <- log10(quant_data_imp_qn)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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parents: 12
diff changeset
876 rownames(quant_data_imp_qn_log) <- rownames(quant_data_imp)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
877
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
878 write_debug_file(quant_data_imp_qn_log)
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
879
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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parents: 0
diff changeset
880 quant_data_imp_qn_ls <- t(scale(t(log10(quant_data_imp_qn))))
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
881
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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parents: 0
diff changeset
882 any_nan <- function(x) {
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
883 !any(x == "NaN")
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
884 }
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
885 sel <- apply(quant_data_imp_qn_ls, 1, any_nan)
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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parents: 0
diff changeset
886 quant_data_imp_qn_ls2 <- quant_data_imp_qn_ls[which(sel), ]
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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parents: 0
diff changeset
887 quant_data_imp_qn_ls2 <- as.data.frame(quant_data_imp_qn_ls2)
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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parents: 12
diff changeset
888 rownames(quant_data_imp_qn_ls2) <- rownames(quant_data_imp)[sel]
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
889
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
890 quant_data_imp_qn_ls <- as.data.frame(quant_data_imp_qn_ls)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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parents: 12
diff changeset
891 rownames(quant_data_imp_qn_ls) <- rownames(quant_data_imp)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
892
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
893 write_debug_file(quant_data_imp_qn_ls)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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parents: 12
diff changeset
894 write_debug_file(quant_data_imp_qn_ls2)
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
895
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
896 #output quantile normalized data
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
897 data_table_imp_qn_lt <- cbind(full_data[1:9], quant_data_imp_qn_log)
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
898 write.table(
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
899 data_table_imp_qn_lt,
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
900 file = imp_qn_lt_data_filenm,
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
901 sep = "\t",
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
902 col.names = TRUE,
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
903 row.names = FALSE,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
904 quote = FALSE
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
905 )
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
906
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
907 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
908
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
909 <!-- ACE insertion begin -->
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
910 ### Checking that normalized, imputed, log-transformed sample distributions are similar:
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
911
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
912 ```{r echo = FALSE, fig.dim = c(9, 5.5), results = 'asis'}
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
913
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
914 # Save unimputed quant_data_log for plotting below
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
915 unimputed_quant_data_log <- quant_data_log
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
916
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
917 # log10 transform (after preparing for zero values,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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parents: 0
diff changeset
918 # which should never happen...)
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
919 quant_data_imp_qn[quant_data_imp_qn == 0] <- .000000001
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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parents: 0
diff changeset
920 quant_data_log <- log10(quant_data_imp_qn)
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
921
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
922 # Output with imputed, un-normalized data
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
923
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
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parents: 12
diff changeset
924 data_table_imputed <- cbind(full_data[1:9], quant_data_imp)
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
925 write.table(
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
926 data_table_imputed
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
927 , file = imputed_data_filename
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
928 , sep = "\t"
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
929 , col.names = TRUE
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
930 , row.names = FALSE
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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parents: 0
diff changeset
931 , quote = FALSE
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
932 )
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
933
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
934 how_many_peptides <- nrow(quant_data_log)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
935
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
936 if ((how_many_peptides) > 0) {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
937 cat(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
938 sprintf(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
939 "Intensities for %d peptides:\n\n\n",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
940 how_many_peptides
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
941 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
942 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
943 cat("\n\n\n")
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
944
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
945
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
946 # data visualization
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
947 old_par <- par(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
948 mai = par("mai") + c(0.5, 0, 0, 0)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
949 , oma = par("oma") + c(0.5, 0, 0, 0)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
950 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
951 # ref: https://r-charts.com/distribution/add-points-boxplot/
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
952 # Vertical plot
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
953 colnames(quant_data_log) <- sample_name_matches
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
954 boxplot(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
955 quant_data_log
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
956 , las = 1
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
957 , col = const_boxplot_fill
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
958 , ylab = latex2exp::TeX("$log_{10}$(peptide intensity)")
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
959 , xlab = "Sample"
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
960 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
961 par(old_par)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
962 } else {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
963 cat("There are no peptides to plot\n")
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
964 }
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
965
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
966 cat("\n\n\n")
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
967
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
968 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
969
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
970 ```{r echo = FALSE, fig.align = "left", fig.dim = c(9, 4), results = 'asis'}
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
971 if (nrow(quant_data_log) > 1) {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
972 quant_data_log_stack <- stack(quant_data_log)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
973 ggplot(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
974 quant_data_log_stack,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
975 aes(x = values)
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
976 ) + xlab(latex2exp::TeX("$log_{10}$(peptide intensity)")) +
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
977 ylab("Probability density") +
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
978 geom_density(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
979 aes(group = ind, colour = ind),
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
980 na.rm = TRUE
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
981 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
982 } else {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
983 cat("No density plot because there are fewer than two peptides to plot.\n\n")
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
984 }
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
985 ```
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
986 ```{r echo = FALSE, results = 'asis'}
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
987 cat("\\leavevmode\\newpage\n")
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
988 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
989
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
990 ## Perform ANOVA Filters
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
991
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
992 ```{r, echo = FALSE}
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
993 # Make new data frame containing only Phosphopeptides
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
994 # to connect preANOVA to ANOVA (connect_df)
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
995 connect_df <- data.frame(
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
996 data_table_imp_qn_lt$Phosphopeptide
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
997 , data_table_imp_qn_lt[, first_data_column]
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
998 )
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
999 colnames(connect_df) <- c("Phosphopeptide", "Intensity")
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1000 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1001
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1002 ```{r echo = FALSE, fig.dim = c(9, 10), results = 'asis'}
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1003 count_of_factor_levels <- length(levels(sample_factor_levels))
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1004 if (count_of_factor_levels < 2) {
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1005 nuke_control_sequences <-
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1006 function(s) {
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1007 s <- gsub("[\\]", "xyzzy_plugh", s)
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1008 s <- gsub("[$]", "\\\\$", s)
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1009 s <- gsub("xyzzy_plugh", "$\\\\backslash$", s)
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1010 return(s)
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1011 }
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1012 cat(
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1013 "ERROR!!!! Cannot perform ANOVA analysis",
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1014 "(see next page)\\newpage\n"
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1015 )
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1016 cat(
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1017 "ERROR: ANOVA analysis",
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1018 "requires two or more factor levels!\n\n\n"
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1019 )
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1020
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1021 cat("\n\n\n\n\n")
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1022 cat("Unparsed sample names are:\n\n\n",
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1023 "\\begin{quote}\n",
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1024 paste(names(quant_data_imp_qn_log), collapse = "\n\n\n"),
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1025 "\n\\end{quote}\n\n")
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1026
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1027 regex_sample_names <- nuke_control_sequences(regex_sample_names)
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1028
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1029 cat("\\leavevmode\n\n\n")
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1030 cat("Parsing rule for SampleNames is",
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1031 "\n\n\n",
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1032 "\\text{'",
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1033 regex_sample_names,
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1034 "'}\n\n\n",
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1035 sep = ""
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1036 )
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1037
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1038 cat("\nParsed sample names are:\n",
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1039 "\\begin{quote}\n",
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1040 paste(sample_name_matches, collapse = "\n\n\n"),
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1041 "\n\\end{quote}\n\n")
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1042
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1043 regex_sample_grouping <- nuke_control_sequences(regex_sample_grouping)
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1044
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1045 cat("\\leavevmode\n\n\n")
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1046 cat("Parsing rule for SampleGrouping is",
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1047 "\n\n\n",
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1048 "\\text{'",
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1049 regex_sample_grouping,
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1050 "'}\n\n\n",
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1051 sep = ""
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1052 )
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1053
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1054 cat("\n\n\n")
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1055 cat("Sample group assignments are:\n",
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1056 "\\begin{quote}\n",
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1057 paste(regmatches(sample_name_matches, m2), collapse = "\n\n\n"),
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1058 "\n\\end{quote}\n\n")
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1059
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1060 } else {
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1061 p_value_data_anova_ps <-
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1062 apply(
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1063 quant_data_imp_qn_log,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1064 1,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1065 anova_func,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1066 grouping_factor = sample_factor_levels
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1067 )
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1068
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1069 p_value_data_anova_ps_fdr <-
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1070 p.adjust(p_value_data_anova_ps, method = "fdr")
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1071 p_value_data <- data.frame(
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1072 phosphopeptide = full_data[, 1]
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1073 ,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1074 raw_anova_p = p_value_data_anova_ps
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1075 ,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1076 fdr_adjusted_anova_p = p_value_data_anova_ps_fdr
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1077 )
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1078
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1079 # output ANOVA file to constructed filename,
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1080 # e.g. "Outputfile_pST_ANOVA_STEP5.txt"
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1081 # becomes "Outpufile_pST_ANOVA_STEP5_FDR0.05.txt"
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1082
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1083 # Re-output datasets to include p-values
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1084 write.table(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1085 cbind(full_data[1:9], p_value_data[, 2:3], quant_data_imp),
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1086 file = imputed_data_filename,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1087 sep = "\t",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1088 col.names = TRUE,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1089 row.names = FALSE,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1090 quote = FALSE
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1091 )
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1092
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1093 write.table(
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1094 cbind(full_data[1:9], p_value_data[, 2:3], quant_data_imp_qn_log),
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1095 file = imp_qn_lt_data_filenm,
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1096 sep = "\t",
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1097 col.names = TRUE,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1098 row.names = FALSE,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1099 quote = FALSE
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1100 )
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1101
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1102
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1103 p_value_data <-
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1104 p_value_data[order(p_value_data$fdr_adjusted_anova_p), ]
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1105
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1106 first_page_suppress <- 1
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1107 number_of_peptides_found <- 0
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1108 cutoff <- val_fdr[1]
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1109 for (cutoff in val_fdr) {
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1110 if (number_of_peptides_found > 49) {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1111 cat("\\leavevmode\n\n\n")
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1112 break
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1113 }
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1114
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1115 #loop through FDR cutoffs
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1116
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1117 filtered_p <-
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1118 p_value_data[
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1119 which(p_value_data$fdr_adjusted_anova_p < cutoff),
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1120 , drop = FALSE
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1121 ]
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1122 filtered_data_filtered <-
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1123 quant_data_imp_qn_log[
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1124 rownames(filtered_p),
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1125 , drop = FALSE
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1126 ]
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1127 filtered_data_filtered <-
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1128 filtered_data_filtered[
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1129 order(filtered_p$fdr_adjusted_anova_p),
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1130 , drop = FALSE
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1131 ]
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1132
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1133 # <!-- ACE insertion start -->
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1134
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1135 if (nrow(filtered_p) && nrow(filtered_data_filtered) > 0) {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1136 if (first_page_suppress == 1) {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1137 first_page_suppress <- 0
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1138 }
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1139 else {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1140 cat("\\newpage\n")
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1141 }
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1142 cat(sprintf(
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1143 "Intensities for %d peptides whose adjusted p-value < %0.2f:\n",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1144 nrow(filtered_data_filtered),
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1145 cutoff
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1146 ))
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1147 cat("\n\n\n")
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1148 cat("\n\n\n")
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1149
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1150 old_oma <- par("oma")
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1151 old_par <- par(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1152 mai = (par("mai") + c(0.7, 0, 0, 0)) * c(1, 1, 0.3, 1),
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1153 oma = old_oma * c(1, 1, 0.3, 1),
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1154 cex.main = 0.9,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1155 cex.axis = 0.7,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1156 fin = c(9, 7.25)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1157 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1158 # ref: https://r-charts.com/distribution/add-points-boxplot/
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1159 # Vertical plot
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1160 colnames(filtered_data_filtered) <- sample_name_matches
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1161 boxplot(
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1162 filtered_data_filtered,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1163 main = "Imputed, normalized intensities", # no line plot
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1164 las = 1,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1165 col = const_boxplot_fill,
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1166 ylab = latex2exp::TeX("$log_{10}$(peptide intensity)")
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1167 )
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1168 par(old_par)
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1169 } else {
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1170 cat(sprintf(
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1171 "%s < %0.2f\n\n\n\n\n",
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1172 "No peptides were found to have cutoff adjusted p-value",
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1173 cutoff
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1174 ))
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1175 }
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1176
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1177 if (nrow(filtered_data_filtered) > 0) {
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1178 #Add Phosphopeptide column to anova_filtered table
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1179 anova_filtered_merge <- merge(
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1180 x = connect_df,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1181 y = filtered_data_filtered,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1182 by.x = "Intensity",
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1183 by.y = 1
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1184 )
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1185 anova_filtered_merge_order <- rownames(filtered_p)
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1186
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1187 anova_filtered_merge_format <- sapply(
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1188 X = filtered_p$fdr_adjusted_anova_p
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1189 ,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1190 FUN = function(x) {
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1191 if (x > 0.0001)
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1192 paste0("(%0.", 1 + ceiling(-log10(x)), "f) %s")
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1193 else
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1194 paste0("(%0.4e) %s")
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1195 }
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1196 )
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1197
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1198 anova_filtered <- data.table(
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1199 anova_filtered_merge$Phosphopeptide
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1200 ,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1201 anova_filtered_merge$Intensity
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1202 ,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1203 anova_filtered_merge[, 2:number_of_samples + 1]
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1204 )
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1205 colnames(anova_filtered) <-
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1206 c("Phosphopeptide", colnames(filtered_data_filtered))
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1207
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1208 # Merge qualitative columns into the ANOVA data
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1209 output_table <- data.frame(anova_filtered$Phosphopeptide)
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1210 output_table <- merge(
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1211 x = output_table,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1212 y = data_table_imp_qn_lt,
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1213 by.x = "anova_filtered.Phosphopeptide",
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1214 by.y = "Phosphopeptide"
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1215 )
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1216
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1217 # Produce heatmap to visualize significance and the effect of imputation
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1218 m <-
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1219 as.matrix(unimputed_quant_data_log[anova_filtered_merge_order, ])
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1220 m_nan_rows <- rowSums(
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1221 matrix(
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1222 as.integer(is.na(m)),
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1223 nrow = nrow(m)
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1224 )
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1225 )
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1226 m <- m[!m_nan_rows, , drop = FALSE]
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1227 if (nrow(m) > 0) {
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1228 rownames_m <- rownames(m)
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1229 rownames(m) <- sapply(
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1230 X = seq_len(nrow(m))
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1231 ,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1232 FUN = function(i) {
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1233 sprintf(
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1234 anova_filtered_merge_format[i],
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1235 filtered_p$fdr_adjusted_anova_p[i],
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1236 rownames_m[i]
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1237 )
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1238 }
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1239 )
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1240 how_many_peptides <- min(50, nrow(m))
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1241 number_of_peptides_found <- how_many_peptides
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1242 if (nrow(m) > 1) {
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1243 m_margin <- m[how_many_peptides:1, ]
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1244 margins <-
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1245 c(max(nchar(colnames(m_margin))) * 10 / 16 # col
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1246 , max(nchar(rownames(m_margin))) * 5 / 16 # row
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1247 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1248 }
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1249
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1250 cat("\\newpage\n")
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1251 if (nrow(m) > 50) {
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1252 cat("Heatmap for the 50 most-significant peptides",
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1253 sprintf(
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1254 "whose adjusted p-value < %0.2f\n",
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1255 cutoff)
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1256 )
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1257 } else {
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1258 if (nrow(m) == 1) {
15
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1259 next
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd"
eschen42
parents: 14
diff changeset
1260 } else {
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1261 cat(
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1262 sprintf("Heatmap for %d usable peptides whose", nrow(m)),
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1263 sprintf("adjusted p-value < %0.2f\n", cutoff)
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1264 )
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1265 }
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1266 }
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1267 cat("\n\n\n")
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1268 cat("\n\n\n")
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1269 try(
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1270 if (nrow(m) > 1) {
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1271 old_oma <- par("oma")
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1272 par(cex.main = 0.6)
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1273 heatmap(
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1274 m[how_many_peptides:1, ],
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1275 Rowv = NA,
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1276 Colv = NA,
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1277 cexRow = 0.7,
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1278 cexCol = 0.8,
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1279 scale = "row",
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1280 margins = margins,
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1281 main =
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1282 "Unimputed, unnormalized intensities",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1283 xlab = "",
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1284 las = 1 #, fin = c(9, 5.5)
12
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1285 )
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1286 }
4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0"
eschen42
parents: 7
diff changeset
1287 )
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
1288 }
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1289 }
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1290 }
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1291 }
13
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50"
eschen42
parents: 12
diff changeset
1292 cat("\\leavevmode\n\n\n")
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
1293 ```