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annotate mqppep_anova_script.Rmd @ 11:254ab97c6a2c draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 681875e344ae25ccd421df12da01bc5521a6a7c7"
author eschen42
date Tue, 15 Mar 2022 12:44:40 +0000
parents d728198f1ba5
children 4deacfee76ef
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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; Nov 16, 2021"
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5 output:
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6 pdf_document: default
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7 params:
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8 inputFile: "test-data/test_input_for_anova.tabular"
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9 alphaFile: "test-data/alpha_levels.tabular"
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10 firstDataColumn: "Intensity"
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11 imputationMethod: !r c("group-median", "median", "mean", "random")[1]
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12 meanPercentile: 1
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13 sdPercentile: 0.2
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14 regexSampleNames: "\\.(\\d+)[A-Z]$"
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15 regexSampleGrouping: "(\\d+)"
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16 imputedDataFilename: "Upstream_Map_pST_outputfile_STEP4_QN_LT.txt"
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17 ---
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18 ```{r setup, include = FALSE}
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19 # ref for parameterizing Rmd document: https://stackoverflow.com/a/37940285
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20 knitr::opts_chunk$set(echo = FALSE, fig.dim = c(9, 10))
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22 ### FUNCTIONS
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24 #ANOVA filter function
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25 anova_func <- function(x, grouping_factor) {
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26 x_aov <- aov(as.numeric(x) ~ grouping_factor)
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27 pvalue <- summary(x_aov)[[1]][["Pr(>F)"]][1]
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28 pvalue
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29 }
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30 ```
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32 ## Purpose:
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33 Perform imputation of missing values, quantile normalization, and ANOVA.
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35 <!--
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36 ## Variables to change for each input file
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37 -->
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38 ```{r include = FALSE}
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39 # Input Filename
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40 input_file <- params$inputFile
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41
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42 # First data column - ideally, this could be detected via regexSampleNames,
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43 # but for now leave it as is.
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44 first_data_column <- params$firstDataColumn
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45 fdc_is_integer <- TRUE
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46 first_data_column <- withCallingHandlers(
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47 as.integer(first_data_column)
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48 , warning = function(w) fdc_is_integer <<- FALSE
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49 )
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50 if (FALSE == fdc_is_integer) {
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51 first_data_column <- params$firstDataColumn
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52 }
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54 # False discovery rate adjustment for ANOVA
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55 # Since pY abundance is low, set to 0.10 and 0.20 in addition to 0.05
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56 val_fdr <-
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57 read.table(file = params$alphaFile, sep = "\t", header = F, quote = "")[, 1]
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59 #Imputed Data filename
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60 imputed_data_filename <- params$imputedDataFilename
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62 #ANOVA data filename
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63 ```
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64
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65 ```{r echo = FALSE}
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66 # Imputation method, should be one of
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67 # "random", "group-median", "median", or "mean"
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68 imputation_method <- params$imputationMethod
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70 # Selection of percentile of logvalue data to set the mean for random number
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71 # generation when using random imputation
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72 mean_percentile <- params$meanPercentile / 100.0
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74 # deviation adjustment-factor for random values; real number.
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75 sd_percentile <- params$sdPercentile
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77 # Regular expression of Sample Names, e.g., "\\.(\\d+)[A-Z]$"
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78 regex_sample_names <- params$regexSampleNames
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80 # Regular expression to extract Sample Grouping from Sample Name;
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81 # if error occurs, compare sample_factor_levels and temp_matches
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82 # to see if groupings/pairs line up
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83 # e.g., "(\\d+)"
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84 regex_sample_grouping <- params$regexSampleGrouping
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85
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86 ```
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87
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88 ```{r echo = FALSE}
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89 ### READ DATA
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90
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91 library(data.table)
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92
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93 # read.table reads a file in table format and creates a data frame from it.
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94 # - note that `quote = ""` means that quotation marks are treated literally.
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95 full_data <- read.table(
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96 file = input_file,
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97 sep = "\t",
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98 header = T,
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99 quote = "",
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100 check.names = FALSE
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101 )
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102 ```
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103
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104 ### Column names from input file
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105
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106 ```{r echo = FALSE, results = 'markup'}
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107 print(colnames(full_data))
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108 data_column_indices <- grep(first_data_column, names(full_data), perl = TRUE)
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109 cat(sprintf("First data column: %d\n", min(data_column_indices)))
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110 cat(sprintf("Last data column: %d\n", max(data_column_indices)))
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111 ```
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112
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113 ```{r echo = FALSE, results = 'asis'}
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114 cat("\\newpage\n")
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115 ```
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116
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117 ### Checking that log-transformed sample distributions are similar:
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118
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119 ```{r echo = FALSE, fig.dim = c(9, 5.5), results = 'asis'}
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120
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121 if (FALSE == fdc_is_integer) {
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122
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123 if (length(data_column_indices) > 0) {
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124 first_data_column <- data_column_indices[1]
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125 } else {
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126 stop(paste("failed to convert firstDataColumn:", first_data_column))
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127 }
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128 }
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129
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130 quant_data0 <- full_data[first_data_column:length(full_data)]
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131 quant_data <- full_data[first_data_column:length(full_data)]
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132 quant_data[quant_data == 0] <- NA #replace 0 with NA
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133 quant_data_log <- log10(quant_data)
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134
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135 rownames(quant_data_log) <- full_data$Phosphopeptide
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136
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137 # data visualization
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138 old_par <- par(
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139 mai = par("mai") + c(0.5, 0, 0, 0)
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140 )
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141 boxplot(
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142 quant_data_log
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143 , las = 2
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144 )
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145 par(old_par)
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146
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147
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148
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149 cat("\\newline\n")
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150 cat("\\newline\n")
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151
0
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152 ```
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153
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154 ```{r echo = FALSE, fig.align = "left", fig.dim = c(9, 4), warning = FALSE}
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155 quant_data_log_stack <- stack(quant_data_log)
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156 library(ggplot2)
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157 ggplot(
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158 quant_data_log_stack,
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159 aes(x = values)) + geom_density(aes(group = ind, colour = ind))
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160 ```
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161
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162 ### Globally, are phosphopeptide intensities are approximately unimodal?
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163
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164 <!--
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165 # ref for bquote below particularly and plotting math expressions generally:
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166 # https://www.r-bloggers.com/2018/03/math-notation-for-r-plot-titles-expression-and-bquote/
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167 -->
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168 ```{r echo = FALSE, fig.align = "left", fig.dim = c(9, 5)}
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169
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170 # identify the location of missing values
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171 fin <- is.finite(as.numeric(as.matrix(quant_data_log)))
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172
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173 logvalues <- as.numeric(as.matrix(quant_data_log))[fin]
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174 plot(
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175 density(logvalues),
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176 main = bquote(
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177 "Smoothed estimated probability density vs." ~ log[10](intensity)),
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178 xlab = bquote(log[10](intensity))
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179 )
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180 hist(
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181 x = as.numeric(as.matrix(quant_data_log))
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182 , breaks = 100
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183 , main = bquote("Frequency vs." ~ log[10](intensity))
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184 , xlab = bquote(log[10](intensity))
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185 )
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186 ```
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187
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188 ### Distribution of standard deviations of phosphopeptides, ignoring missing values:
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189
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190 ```{r echo = FALSE, fig.align = "left", fig.dim = c(9, 5)}
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191 # determine quantile
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192 q1 <- quantile(logvalues, probs = mean_percentile)[1]
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193
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194 # determine standard deviation of quantile to impute
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195 sd_finite <- function(x) {
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196 ok <- is.finite(x)
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197 sd(x[ok]) * sd_percentile
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198 }
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199 # 1 = row of matrix (ie, phosphopeptide)
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200 sds <- apply(quant_data_log, 1, sd_finite)
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201 plot(
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202 density(sds, na.rm = T)
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203 , main = "Smoothed estimated probability density vs. std. deviation"
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204 , sub = "(probability estimation made with Gaussian smoothing)"
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205 )
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206
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207 m1 <- median(sds, na.rm = T) #sd to be used is the median sd
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208
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209 ```
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210
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211
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212
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213 <!--
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214 The number of missing values are:
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215 -->
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216 ```{r echo = FALSE}
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217 #Determine number of cells to impute
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218 temp <- quant_data[is.na(quant_data)]
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219
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220 #Determine number of values to impute
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221 number_to_impute <- length(temp)
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222 ```
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223
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224 <!--
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225 % of values that are missing:
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226 -->
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227 ```{r echo = FALSE}
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228 pct_missing_values <- length(temp) / (length(logvalues) + length(temp)) * 100
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229 ```
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230
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231 <!--
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232 First few rows of data before imputation:
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233 -->
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234 ```{r echo = FALSE, results = 'asis'}
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235 cat("\\newpage\n")
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236 ```
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237
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238 ## Parse sample names
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239
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240 Parse the names of the samples to deduce the factor level for each sample:
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241
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242 ```{r echo = FALSE}
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243
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244 # prep for trt-median based imputation
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245
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246 # Assuming that regex_sample_names <- "\\.(\\d+)[A-Z]$"
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247 # get factors ->
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248 # group runs (samples) by ignoring terminal [A-Z] in sample names
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249
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250 m <- regexpr(regex_sample_names, names(quant_data), perl = TRUE)
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251 temp_matches <- regmatches(names(quant_data), m)
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252 print("Extracted sample names")
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253 print(temp_matches)
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254 m2 <- regexpr(regex_sample_grouping, temp_matches, perl = TRUE)
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255 sample_factor_levels <- as.factor(regmatches(temp_matches, m2))
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256 print("Factor levels")
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257 print(sample_factor_levels)
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258
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259 ```
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260 ## Impute missing values
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261
0
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262 ```{r echo = FALSE}
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263
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264 #Determine number of cells to impute
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265 cat("Before imputation,",
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266 sprintf(
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267 "there are:\n %d peptides\n %d missing values (%2.0f%s)",
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268 sum(rep.int(TRUE, nrow(quant_data))),
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269 sum(is.na(quant_data)),
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270 pct_missing_values,
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271 "%"
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272 )
0
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273 )
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274
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275 ```
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276 ```{r echo = FALSE}
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277
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278 #Impute data
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279 quant_data_imp <- quant_data
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280
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281 # Identify which values are missing and need to be imputed
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282 ind <- which(is.na(quant_data_imp), arr.ind = TRUE)
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283
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284 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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285 ```{r echo = FALSE}
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286
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287 # Apply imputation
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288 switch(
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289 imputation_method
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290 , "group-median" = {
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291 cat("Imputation method:\n substitute missing value",
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292 "with median peptide-intensity for sample-group\n")
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293
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294 sample_level_integers <- as.integer(sample_factor_levels)
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295 for (i in seq_len(length(levels(sample_factor_levels)))) {
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296 level_cols <- i == sample_level_integers
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297 ind <- which(is.na(quant_data_imp[, level_cols]), arr.ind = TRUE)
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298 quant_data_imp[ind, level_cols] <-
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299 apply(quant_data_imp[, level_cols], 1, median, na.rm = T)[ind[, 1]]
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300 }
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301 good_rows <- !is.na(rowMeans(quant_data_imp))
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302 }
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303 , "median" = {
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304 cat("Imputation method:\n substitute missing value with",
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305 "median peptide-intensity across all sample classes\n")
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306 quant_data_imp[ind] <- apply(quant_data_imp, 1, median, na.rm = T)[ind[, 1]]
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307 good_rows <- !is.na(rowMeans(quant_data_imp))
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308 }
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309 , "mean" = {
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310 cat("Imputation method:\n substitute missing value with",
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311 "mean peptide-intensity across all sample classes\n")
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312 quant_data_imp[ind] <- apply(quant_data_imp, 1, mean, na.rm = T)[ind[, 1]]
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313 good_rows <- !is.na(rowMeans(quant_data_imp))
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314 }
7
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315 , "random" = {
0
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316 cat(
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317 "Imputation method:\n substitute missing value with\n ",
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318 sprintf(
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319 "random intensity N ~ (%0.2f, %0.2f)\n"
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320 , q1, m1
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321 )
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322 )
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323 quant_data_imp[is.na(quant_data_imp)] <-
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324 10 ^ rnorm(number_to_impute, mean = q1, sd = m1)
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325 good_rows <- !is.na(rowMeans(quant_data_imp))
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326 }
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327 )
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328
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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329 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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330 ```{r echo = FALSE}
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331
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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332 #Determine number of cells to impute
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333 temp <- quant_data_imp[is.na(quant_data_imp)]
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334 cat("After imputation, there are:",
0
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335 sprintf(
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336 "\n %d missing values\n %d usable peptides analysis"
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337 , sum(is.na(quant_data_imp[good_rows, ]))
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338 , sum(good_rows)
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339 ),
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340 sprintf(
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341 "\n %d peptides with too many missing values for further analysis"
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342 , sum(!good_rows)
0
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343 )
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344 )
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345 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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346 ```{r echo = FALSE}
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347
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348
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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349 # Zap rows where imputation was ineffective
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350 full_data <- full_data [good_rows, ]
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351 quant_data <- quant_data [good_rows, ]
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352 quant_data_imp <- quant_data_imp[good_rows, ]
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353
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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354 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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355 ```{r echo = FALSE}
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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356
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357 d_combined <- (density(as.numeric(as.matrix(
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358 log10(quant_data_imp)
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359 ))))
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360 d_original <-
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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361 density(as.numeric(as.matrix(
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362 log10(quant_data_imp[!is.na(quant_data)]))))
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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363
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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364 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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365 ```{r echo = FALSE}
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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366
7
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367 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"
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368 # There ARE missing values
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369 d_imputed <-
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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370 (density(as.numeric(as.matrix(
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371 log10(quant_data_imp[is.na(quant_data)])
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372 ))))
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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373 } else {
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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374 # There are NO missing values
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375 d_imputed <- d_combined
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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376 }
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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377
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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378 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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379
7
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380 ```{r echo = FALSE, fig.dim = c(9, 5)}
0
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381 ylim <- c(0, max(d_combined$y, d_original$y, d_imputed$y))
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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382 plot(
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383 d_combined,
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384 ylim = ylim,
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385 sub = "Blue = data before imputation; Red = imputed data",
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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386 main = "Density vs. log10(intensity) before and after imputation"
0
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387 )
7
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388 lines(d_original, col = "blue")
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389 lines(d_imputed, col = "red")
0
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390 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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391
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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392 ## Perform Quantile Normalization
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393
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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394 <!--
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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395 # 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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396 # ---
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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397 # 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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398 # 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"
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399 # 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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400 # ```
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401 # BiocManager::install("preprocessCore", configure.args="--disable-threading", force = TRUE, lib=.libPaths()[1])
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402 # ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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403 # 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"
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404 # 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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405 # ...
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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406 # ---
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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407 # 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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408 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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409 # Description:
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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410 # 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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411 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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412 # Usage:
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413 # normalize.quantiles(x, copy = TRUE, keep.names = FALSE)
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414 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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415 # Arguments:
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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416 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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417 # - 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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418 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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419 # - 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"
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420 # 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"
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421 # it in place will be more memory friendly.
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422 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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423 # - 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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424 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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425 # Details:
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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426 # 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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427 # 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"
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428 # please cite Bolstad et al, Bioinformatics (2003).
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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429 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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430 # 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"
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431 # 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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432 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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433 # 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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434 # 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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435 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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436 # 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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437 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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438 # 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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439 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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440 # References
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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441 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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442 # - 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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443 # 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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444 #
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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445 # - 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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446 # 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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447 # 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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448 # 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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449 # ...
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450 -->
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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451 ```{r echo = FALSE}
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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452 library(preprocessCore)
0
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453
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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454 if (TRUE) {
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455 quant_data_imp_qn <- normalize.quantiles(as.matrix(quant_data_imp))
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456 } else {
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457 quant_data_imp_qn <- as.matrix(quant_data_imp)
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458 }
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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459
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460 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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461 names(quant_data_imp_qn) <- names(quant_data_imp)
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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462 quant_data_imp_qn_log <- log10(quant_data_imp_qn)
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463
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464 rownames(quant_data_imp_qn_log) <- full_data[, 1]
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465
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466 quant_data_imp_qn_ls <- t(scale(t(log10(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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467 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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468 !any(x == "NaN")
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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469 }
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470 sel <- apply(quant_data_imp_qn_ls, 1, any_nan)
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471 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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472 quant_data_imp_qn_ls2 <- as.data.frame(quant_data_imp_qn_ls2)
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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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473
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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474 #output quantile normalized data
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475 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"
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476 write.table(
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477 data_table_imp_qn_lt,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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478 file = paste(paste(
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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479 strsplit(imputed_data_filename, ".txt"), "QN_LT", sep = "_"
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480 ), ".txt", sep = ""),
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481 sep = "\t",
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482 col.names = TRUE,
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483 row.names = FALSE
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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484 )
0
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485
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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486 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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487
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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488 <!-- ACE insertion begin -->
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489 ### 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"
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490
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491 ```{r echo = FALSE, fig.dim = c(9, 5.5), results = 'asis'}
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492
0
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493
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494 # Save unimputed quant_data_log for plotting below
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495 unimputed_quant_data_log <- quant_data_log
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496
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497 # log10 transform (after preparing for zero values,
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498 # which should never happen...)
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499 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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500 quant_data_log <- log10(quant_data_imp_qn)
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501
7
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502 # Output quantile-normalized log-transformed dataset
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503 # with imputed, normalized data
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504
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
505 data_table_imputed <- cbind(full_data[1:9], quant_data_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
506 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
507 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
508 , 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
509 , sep = "\t"
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
510 , 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
511 , 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
512 , quote = FALSE
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
513 )
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
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
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
516
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
517 # data visualization
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
518 old_par <- par(
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
519 mai = par("mai") + c(0.5, 0, 0, 0)
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
520 , oma = par("oma") + c(0.5, 0, 0, 0)
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
521 )
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
522 boxplot(
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
523 quant_data_log
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
524 , las = 2
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
525 )
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
526 par(old_par)
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
527
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
528
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
529
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
530 cat("\\newline\n")
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
531 cat("\\newline\n")
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
532
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
533 ```
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 ```{r echo = FALSE, fig.align = "left", fig.dim = c(9, 4)}
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
536 quant_data_log_stack <- stack(quant_data_log)
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
537 ggplot(
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
538 quant_data_log_stack,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
539 aes(x = values)
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
540 ) + geom_density(aes(group = ind, colour = ind))
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
541 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
542
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
543 ## Perform ANOVA filters
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
544
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
545 (see following pages)
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
546
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
547 ```{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
548 # 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
549 # 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
550 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
551 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
552 , 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
553 )
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
554 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
555 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
556
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
557 ```{r echo = FALSE, fig.dim = c(9, 10), results = 'asis'}
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
558 # Get factors -> group replicates (as indicated by terminal letter)
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
559 # by the preceding digits;
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
560 # e.g., group .1A .1B .1C into group 1; .2A .2B .2C, into group 2; etc..
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
561 m <-
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
562 regexpr(regex_sample_names, names(quant_data_imp_qn_log), perl = TRUE)
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
563
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
564 temp_matches <- regmatches(names(quant_data_imp_qn_log), m)
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
565
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
566 number_of_samples <- length(temp_matches)
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
567
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
568 m2 <- regexpr(regex_sample_grouping, temp_matches, perl = TRUE)
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
569
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
570
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
571 sample_factor_levels <- as.factor(regmatches(temp_matches, m2))
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
572
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
573
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
574 if (length(levels(sample_factor_levels)) < 2) {
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
575 cat(
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
576 "ERROR!!!! Cannot perform ANOVA analysis",
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
577 "because it requires two or more factor levels\n"
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
578 )
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
579 cat("Unparsed sample names are:\n")
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
580 print(names(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
581 cat(sprintf("Parsing rule for SampleNames is '%s'\n", regex_sample_names))
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
582 cat("Parsed names are:\n")
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
583 print(temp_matches)
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
584 cat(sprintf(
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
585 "Parsing rule for SampleGrouping is '%s'\n",
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
586 regex_sample_grouping
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
587 ))
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
588 cat("Sample group assignments are:\n")
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
589 print(regmatches(temp_matches, m2))
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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diff changeset
590 } else {
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
591 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
592 apply(
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
593 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
594 1,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
595 anova_func,
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
596 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
597 )
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
598
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
599 p_value_data_anova_ps_fdr <-
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
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diff changeset
600 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"
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parents: 0
diff changeset
601 p_value_data <- data.frame(
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
602 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
603 ,
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
604 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
605 ,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
606 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
607 )
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
608
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
609 # output ANOVA file to constructed filename,
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
610 # 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
611 # 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
612
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
613 # Re-output quantile-normalized log-transformed dataset
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
614 # with imputed, normalized data to include p-values
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
615
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
616 data_table_imputed <-
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
617 cbind(full_data[1:9], p_value_data[, 2:3], 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
618 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
619 data_table_imputed,
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
620 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
621 sep = "\t",
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
622 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
623 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
624 quote = FALSE
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
625 )
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
626
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
627
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
628 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
629 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
630
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
631 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
632 for (cutoff in val_fdr) {
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
633 #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
634
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
635 filtered_p <-
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
636 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
637 which(p_value_data$fdr_adjusted_anova_p < cutoff),
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
638 ,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
639 drop = FALSE
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
640 ]
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
641 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
642 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
643 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
644 ,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
645 drop = FALSE
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
646 ]
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
647 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
648 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
649 order(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
650 ,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
651 drop = FALSE
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
652 ]
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
653
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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parents:
diff changeset
654 # <!-- ACE insertion start -->
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
655 old_oma <- par("oma")
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
656 old_par <- par(
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
657 mai = (par("mai") + c(0.7, 0, 0, 0)) * c(1, 1, 0.3, 1),
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
658 oma = old_oma * c(1, 1, 0.3, 1),
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
659 cex.main = 0.9,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
660 cex.axis = 0.7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
661 )
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
662
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
663 cat("\\newpage\n")
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
664 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
665 cat(sprintf(
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
666 "Intensities for peptides whose adjusted p-value < %0.2f\n",
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
667 cutoff
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
668 ))
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
669 cat("\\newline\n")
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
670 cat("\\newline\n")
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
671
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
672 boxplot(
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
673 filtered_data_filtered,
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
674 main = "Imputed, normalized intensities", # no line plot
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
675 las = 2,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
676 ylab = expression(log[10](intensity))
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
677 )
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
678 } else {
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
679 cat(sprintf(
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
680 "No peptides were found to have cutoff adjusted p-value < %0.2f\n",
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
681 cutoff
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
682 ))
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
683 }
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
684 par(old_par)
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
685
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
686 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
687 #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
688 anova_filtered_merge <- merge(
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
689 x = connect_df
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
690 ,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
691 y = 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
692 ,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
693 by.x = "Intensity"
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
694 ,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
695 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
696 )
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
697 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
698
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
699 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
700 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
701 ,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
702 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
703 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
704 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
705 else
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
706 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
707 }
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
708 )
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
709
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
710
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
711
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
712 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
713 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
714 ,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
715 anova_filtered_merge$Intensity
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
716 ,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
717 anova_filtered_merge[, 2:number_of_samples + 1]
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
718 )
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
719 colnames(anova_filtered) <-
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
720 c("Phosphopeptide", colnames(filtered_data_filtered))
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
721
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
722 # merge qualitative columns into the ANOVA data
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
723 output_table <- data.frame(anova_filtered$Phosphopeptide)
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
724 output_table <- merge(
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
725 x = output_table
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
726 ,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
727 y = data_table_imp_qn_lt
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
728 ,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
729 by.x = "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
730 ,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
731 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
732 )
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
733
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
734 #Produce heatmap to visualize significance and the effect of imputation
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
735 m <-
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
736 as.matrix(unimputed_quant_data_log[anova_filtered_merge_order, ])
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
737 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
738 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
739 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
740 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
741 ,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
742 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
743 sprintf(
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
744 anova_filtered_merge_format[i]
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
745 ,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
746 filtered_p$fdr_adjusted_anova_p[i]
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
747 ,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
748 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
749 )
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
750 }
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
751 )
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
752 margins <- c(max(nchar(colnames(m))) * 10 / 16 # col
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
753 , max(nchar(rownames(m))) * 5 / 16 # row
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
754 )
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
755 how_many_peptides <- min(50, nrow(m))
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
756
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
757 cat("\\newpage\n")
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
758 if (nrow(m) > 50) {
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
759 cat("Heatmap for the 50 most-significant peptides",
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
760 sprintf(
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
761 "whose adjusted p-value < %0.2f\n",
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
762 cutoff)
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
763 )
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
764 } else {
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
765 cat("Heatmap for peptides whose",
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
766 sprintf("adjusted p-value < %0.2f\n",
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
767 cutoff)
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
768 )
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
769 }
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
770 cat("\\newline\n")
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
771 cat("\\newline\n")
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
772 op <- par("cex.main")
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
773 try(
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
774 if (nrow(m) > 1) {
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
775 par(cex.main = 0.6)
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
776 heatmap(
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
777 m[how_many_peptides:1, ],
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
778 Rowv = NA,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
779 Colv = NA,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
780 cexRow = 0.7,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
781 cexCol = 0.8,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
782 scale = "row",
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
783 margins = margins,
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
784 main =
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
785 "Heatmap of unimputed, unnormalized intensities",
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
786 xlab = ""
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
787 )
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
788 }
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
789 )
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
790 par(op)
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
791 }
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
792 }
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
793 }
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
794 }
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
795 ```
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
796
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
797 <!--
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
798 ## Peptide IDs, etc.
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
799
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
eschen42
parents:
diff changeset
800 See output files.
7
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637"
eschen42
parents: 0
diff changeset
801 -->