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annotate masigpro.R @ 4:402e0b9cfd87 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 7dc16d5d4169a8fbfb3fad3b2212fd8b6d481f5f"
author iuc
date Sat, 27 Nov 2021 09:58:07 +0000
parents db04ba860dab
children
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cc96abdef027 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256
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1 #!/usr/bin/env Rscript
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cc96abdef027 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256
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3 # A command-line interface to maSigPro for use with Galaxy
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4 # written by Clemens Blank.
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5 # Thanks to Bjoern Gruening and Michael Love for their DESeq2
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6 # wrapper as a basis to build upon.
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8 # setup R error handling to go to stderr
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9 error_foo <- function() {
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10 cat(geterrmessage(), file = stderr());
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11 q("no", 1, F)
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12 }
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13 options(show.error.messages = F, error = error_foo)
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cc96abdef027 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256
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15 # we need that to not crash galaxy with an UTF8 error on German LC settings.
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16 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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18 suppressPackageStartupMessages({
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19 library("maSigPro")
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20 library("optparse")
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21 library("mclust")
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22 })
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24 # The following code fixes an error in the stepback function
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25 # of the maSigPro package. This code is hopefully temporary
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26 # and can be removed if the fix is included in a future
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27 # version. The stepback function in the maSigPro namespace
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28 # will be overwritten by the following function.
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29 stepback <- function(y = y, d = d, alfa = 0.05, family = gaussian(), epsilon=0.00001) {
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30 lm1 <- glm(y ~ ., data = d, family = family, epsilon = epsilon)
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31 result <- summary(lm1)
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32 max <- max(result$coefficients[, 4][-1], na.rm = TRUE)
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33 if (length(result$coefficients[, 4][-1]) == 1) {
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34 if (max > alfa) {
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35 max <- 0
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36 lm1 <- glm(y ~ 1, family = family, epsilon = epsilon)
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37 }
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38 }
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39 while (max > alfa) {
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40 varout <- names(result$coefficients[, 4][-1])[result$coefficients[, 4][-1] == max][1]
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41 pos <- position(matrix = d, vari = varout)
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42 d <- d[, -pos]
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43 if (length(result$coefficients[, 4][-1]) == 2) {
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44 min <- min(result$coefficients[, 4][-1], na.rm = TRUE)
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45 lastname <- names(result$coefficients[, 4][-1])[result$coefficients[, 4][-1] == min]
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46 }
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47 if (is.null(dim(d))) {
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48 d <- as.data.frame(d)
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49 colnames(d) <- lastname
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50 }
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51 lm1 <- glm(y ~ ., data = d, family = family, epsilon = epsilon)
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52 result <- summary(lm1)
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53 max <- max(result$coefficients[, 4][-1], na.rm = TRUE)
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54 if (length(result$coefficients[, 4][-1]) == 1) {
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55 max <- result$coefficients[, 4][-1]
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56 if (max > alfa) {
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57 max <- 0
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58 lm1 <- glm(y ~ 1, family = family, epsilon = epsilon)
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59 }
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60 }
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61 }
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62 return(lm1)
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63 }
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64
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65 unlockBinding("stepback", as.environment("package:maSigPro"))
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66 assignInNamespace("stepback", stepback, ns = "maSigPro", envir = as.environment("package:maSigPro"))
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67 assign("stepback", stepback, as.environment("package:maSigPro"))
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68 lockBinding("stepback", as.environment("package:maSigPro"))
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69 # End of temporary code to fix stepback.R
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70
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71 options(stringAsFactors = FALSE, useFancyQuotes = FALSE)
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72 args <- commandArgs(trailingOnly = TRUE)
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73
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74 # specify our desired options in a list
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75 # by default OptionParser will add an help option equivalent to
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76 # make_option(c("-h", "--help"), action="store_true", default=FALSE,
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77 # help="Show this help message and exit")
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78 option_list <- list(
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79 make_option(c("-q", "--quiet"), action = "store_false",
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80 dest = "verbose", help = "Print little output"),
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81 make_option(c("-e", "--edesign"), type = "character"),
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82 make_option(c("-d", "--data"), type = "character"),
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83 make_option(c("-o", "--outfile"), type = "character"),
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84 make_option("--degree", type = "integer", default = 1),
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85 make_option("--time_col", type = "integer", default = 1),
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86 make_option("--repl_col", type = "integer", default = 2),
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87 make_option("--qvalue", type = "double", default = 0.05),
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88 make_option("--min_obs", type = "integer", default = 6),
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89 make_option("--step_method", type = "character", default = "backward"),
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90 make_option("--nvar_correction", type = "logical", default = FALSE),
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91 make_option("--alfa", type = "double", default = 0.05),
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92 make_option("--rsq", type = "double", default = 0.7),
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93 make_option("--vars", type = "character", default = "groups"),
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94 make_option("--significant_intercept", type = "character", default = "dummy"),
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95 make_option("--cluster_data", type = "integer", default = 1),
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96 make_option(c("-k", "--k"), type = "integer", default = 9),
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97 make_option("--print_cluster", type = "logical", default = FALSE),
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98 make_option("--cluster_method", type = "character", default = "hclust"),
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99 make_option("--distance", type = "character", default = "cor"),
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100 make_option("--agglo_method", type = "character", default = "ward.D"),
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101 make_option("--iter_max", type = "integer", default = 500),
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102 make_option("--color_mode", type = "character", default = "rainbow"),
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103 make_option("--show_fit", type = "logical", default = TRUE),
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104 make_option("--show_lines", type = "logical", default = TRUE),
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105 make_option("--cexlab", type = "double", default = 0.8),
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106 make_option("--legend", type = "logical", default = TRUE)
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107 )
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108
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109 # get command line options, if help option encountered print help and exit,
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110 # otherwise if options not found on command line then set defaults
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111 opt <- parse_args(OptionParser(option_list = option_list))
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112
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113 # enforce the following required arguments
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114 if (is.null(opt$edesign)) {
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115 cat("'edesign' is required\n")
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116 q(status = 1)
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117 }
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118 if (is.null(opt$data)) {
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119 cat("'data' is required\n")
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120 q(status = 1)
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121 }
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122 if (is.null(opt$outfile)) {
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123 cat("'outfile' is required\n")
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124 q(status = 1)
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125 }
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126
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127 verbose <- if (is.null(opt$quiet)) {
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128 TRUE
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129 } else {
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130 FALSE
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131 }
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132
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133 edesign <- as.matrix(read.table(opt$edesign, header = TRUE, row.names = 1))
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134
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135 data <- read.table(opt$data, header = TRUE, check.names = FALSE)
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136
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137 results <- maSigPro(data, edesign, degree = opt$degree, time.col = opt$time_col,
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138 repl.col = opt$repl_col, Q = opt$qvalue, min.obs = opt$min_obs,
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139 step.method = opt$step_method, nvar.correction = opt$nvar_correction,
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140 alfa = opt$alfa, rsq = opt$rsq, vars = opt$vars,
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141 significant.intercept = opt$significant_intercept,
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142 cluster.data = opt$cluster_data, k = opt$k,
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143 cluster.method = opt$cluster_method, distance = opt$distance,
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144 agglo.method = opt$agglo_method, iter.max = opt$iter_max,
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145 color.mode = opt$color_mode, show.fit = opt$show_fit,
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146 show.lines = opt$show_lines, cexlab = opt$cexlab,
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147 legend = opt$legend)
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148
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149 if (opt$print_cluster) {
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150 for (i in seq_len(length(results$sig.genes))) {
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151 colname <- paste(names(results$sig.genes)[i], "cluster", sep = "_")
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152 results$summary[colname] <- ""
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153 results$summary[[colname]][seq_len(length(results$sig.genes[[i]]$sig.profiles$`cluster$cut`))] <-
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154 results$sig.genes[[i]]$sig.profiles$`cluster$cut`
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155 }
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156 }
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157
1
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158 filename <- opt$outfile
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159
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160 write.table((results$summary), file = filename, sep = "\t", quote = FALSE,
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161 row.names = FALSE, col.names = TRUE)
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162
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163 cat("Session information:\n\n")
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164
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165 sessionInfo()