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annotate sleuth.R @ 0:a9d7ab1986ca draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
author iuc
date Thu, 01 Jun 2023 07:55:48 +0000
parents
children 9a58bef001d5
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a9d7ab1986ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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1 library(sleuth,
a9d7ab1986ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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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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7
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8
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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
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29 parser$add_argument("--factorLevel", action = "append", required = TRUE)
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30 parser$add_argument("--factorLevel_counts",
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31 action = "append",
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32 required = TRUE)
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33 parser$add_argument("--factorLevel_n", action = "append", required = TRUE)
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34 parser$add_argument("--cores", type = "integer", required = TRUE)
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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 = TRUE)
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37 parser$add_argument("--lwr", type = "numeric", required = TRUE)
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38 parser$add_argument("--upr", type = "numeric", required = TRUE)
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39
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40 args <- parser$parse_args()
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41
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42 all_files <- args$factorLevel_counts
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43
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44 conditions <- c()
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45 for (x in seq_along(args$factorLevel)) {
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46 temp <- append(conditions, rep(args$factorLevel[[x]]))
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47 conditions <- temp
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48 }
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49
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50 sample_names <- all_files %>%
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51 str_replace(pattern = "\\.tab", "")
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52
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53 design <-
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54 data.frame(list(
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55 sample = sample_names,
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56 condition = conditions,
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57 path = all_files
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58 ))
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59 so <- sleuth_prep(design,
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60 cores = args$cores,
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61 normalize = args$normalize)
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62
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63 so <- sleuth_fit(
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64 so,
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65 ~ condition,
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66 "full",
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67 n_bins = args$nbins,
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68 lwr = args$lwr,
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69 upr = args$upr
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70 )
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71
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72 so <- sleuth_fit(
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73 so,
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74 ~ 1,
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75 "reduced",
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76 n_bins = args$nbins,
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77 lwr = args$lwr,
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78 upr = args$upr
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79 )
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80
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81 so <- sleuth_lrt(so, "reduced", "full")
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82
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83 sleuth_table <-
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84 sleuth_results(so, "reduced:full", "lrt", show_all = FALSE)
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85
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86 write.table(
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87 sleuth_table,
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88 file = "sleuth_table.tab",
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89 quote = FALSE,
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90 sep = "\t",
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91 col.names = TRUE,
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92 row.names = FALSE
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93 )
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94
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95
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96 outputFile <- file.path(getwd(), "pca_plot.pdf")
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97 pdf(file = outputFile,
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98 height = 6,
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99 width = 9)
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100 plot_pca(so, color_by = "condition")
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101 dev.off()
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102
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103 outputFile <- file.path(getwd(), "group_density.pdf")
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104 pdf(file = outputFile,
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105 height = 6,
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106 width = 9)
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107 plot_group_density(
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108 so,
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109 use_filtered = TRUE,
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110 units = "est_counts",
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111 trans = "log",
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112 grouping = setdiff(colnames(so$sample_to_covariates),
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113 "sample"),
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114 offset = 1
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115 )
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116 dev.off()