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annotate sleuth.R @ 1:9a58bef001d5 draft

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author iuc
date Wed, 07 Jun 2023 11:47:17 +0000
parents a9d7ab1986ca
children c3c48adf78cf
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1 library(sleuth,
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2 quietly = TRUE,
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3 warn.conflicts = FALSE)
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4 library(annotables, quietly = TRUE, warn.conflicts = FALSE)
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5 library(argparse, quietly = TRUE, warn.conflicts = FALSE)
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6 library(tidyverse)
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9 # setup R error handling to go to stderr
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10 options(
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11 show.error.messages = FALSE,
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12 error = function() {
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13 cat(geterrmessage(), file = stderr())
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14 q("no", 1, FALSE)
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15 }
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16 )
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18 # we need that to not crash galaxy with an UTF8 error on German LC settings.
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19 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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21 ################################################################################
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22 ### Input Processing
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23 ################################################################################
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26 # Collect arguments from command line
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27 parser <- ArgumentParser(description = "Sleuth R script")
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28
1
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29 parser$add_argument("--factorLevel", action = "append", required = FALSE)
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30 parser$add_argument("--factorLevel_counts",
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31 action = "append",
1
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32 required = FALSE)
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33 parser$add_argument("--factorLevel_n", action = "append", required = FALSE)
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34 parser$add_argument("--cores", type = "integer", required = FALSE)
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35 parser$add_argument("--normalize", action = "store_true", required = FALSE)
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36 parser$add_argument("--nbins", type = "integer", required = FALSE)
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37 parser$add_argument("--lwr", type = "numeric", required = FALSE)
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38 parser$add_argument("--upr", type = "numeric", required = FALSE)
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39 parser$add_argument("--metadata_file",
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40 action = "append",
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41 required = FALSE)
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42 parser$add_argument("--experiment_design", required = FALSE)
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44 args <- parser$parse_args()
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45
1
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46 if (args$experiment_design == "complex") {
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47 ## Complex experiment design
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48 ############################
0
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49
1
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50 s2c <-
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51 read.table(file = args$metadata_file,
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52 header = TRUE,
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53 sep = "\t")
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54 paths <- c()
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55 for (x in s2c$data_filename) {
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56 paths <- c(paths, paste("./kallisto_outputs/", x, sep = ""))
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57 }
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58 for (f in paths) {
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59 file.rename(f, gsub(".fastq.*", "", f))
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60 file.rename(f, paste(gsub(".fastq.*", "", f), ".h5", sep = ""))
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61 }
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62 s2c$path <- paste(gsub(".fastq.*", ".h5", paths), ".h5", sep = "")
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63
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64 so <- sleuth_prep(s2c, full_model = ~ condition, num_cores = 1)
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65 so <- sleuth_fit(so)
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66
1
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67 } else {
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68 ## Simple experiment design
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69 ###########################
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70
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71 conditions <- c()
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72 for (x in seq_along(args$factorLevel)) {
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73 temp <- append(conditions, rep(args$factorLevel[[x]]))
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74 conditions <- temp
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75 }
0
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76
1
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77 sample_names <-
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78 gsub(".fastq.+", "", basename(args$factorLevel_counts))
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79
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80 design <-
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81 data.frame(list(
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82 sample = sample_names,
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83 condition = conditions,
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84 path = args$factorLevel_counts
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85 ))
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86 so <- sleuth_prep(design,
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87 cores = args$cores,
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88 normalize = args$normalize)
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89 }
0
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90
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91 so <- sleuth_fit(
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92 so,
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93 ~ condition,
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94 "full",
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95 n_bins = args$nbins,
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96 lwr = args$lwr,
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97 upr = args$upr
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98 )
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99
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100 so <- sleuth_fit(
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101 so,
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102 ~ 1,
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103 "reduced",
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104 n_bins = args$nbins,
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105 lwr = args$lwr,
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106 upr = args$upr
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107 )
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108
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109 so <- sleuth_lrt(so, "reduced", "full")
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110
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111 sleuth_table <-
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112 sleuth_results(so, "reduced:full", "lrt", show_all = FALSE)
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113
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114 write.table(
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115 sleuth_table,
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116 file = "sleuth_table.tab",
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117 quote = FALSE,
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118 sep = "\t",
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119 col.names = TRUE,
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120 row.names = FALSE
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121 )
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122
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123
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124 outputFile <- file.path(getwd(), "pca_plot.pdf")
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125 pdf(file = outputFile,
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126 height = 6,
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127 width = 9)
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128 plot_pca(so, color_by = "condition")
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129 dev.off()
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130
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131 outputFile <- file.path(getwd(), "group_density.pdf")
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132 pdf(file = outputFile,
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133 height = 6,
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134 width = 9)
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135 plot_group_density(
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136 so,
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137 use_filtered = TRUE,
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138 units = "est_counts",
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139 trans = "log",
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140 grouping = setdiff(colnames(so$sample_to_covariates),
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141 "sample"),
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142 offset = 1
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143 )
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144 dev.off()