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annotate masigpro.R @ 3:83f8b5ceff43 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 60951bbe9b08fa6eb2762db9ee15c88e8acf1a1f"
author iuc
date Tue, 03 Dec 2019 06:18:47 -0500
parents db04ba860dab
children 402e0b9cfd87
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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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cc96abdef027 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256
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8 # setup R error handling to go to stderr
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9 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
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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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11 # we need that to not crash galaxy with an UTF8 error on German LC settings.
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12 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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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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14 suppressPackageStartupMessages({
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15 library("maSigPro")
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16 library("optparse")
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17 library("mclust")
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18 })
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20 # The following code fixes an error in the stepback function
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21 # of the maSigPro package. This code is hopefully temporary
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22 # and can be removed if the fix is included in a future
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23 # version. The stepback function in the maSigPro namespace
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24 # will be overwritten by the following function.
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25 stepback <- function (y = y, d = d, alfa = 0.05, family = gaussian() , epsilon=0.00001)
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26 {
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27 lm1 <- glm(y ~ ., data = d, family=family, epsilon=epsilon)
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28 result <- summary(lm1)
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29 max <- max(result$coefficients[, 4][-1], na.rm = TRUE)
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30 if (length(result$coefficients[, 4][-1]) == 1) {
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31 if (max > alfa) {
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32 max = 0
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33 lm1 <- glm(y ~ 1, family=family, epsilon=epsilon)
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34 }
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35 }
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36 while (max > alfa) {
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37 varout <- names(result$coefficients[, 4][-1])[result$coefficients[,
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38 4][-1] == max][1]
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39 pos <- position(matrix = d, vari = varout)
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40 d <- d[, -pos]
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41 if (length(result$coefficients[, 4][-1]) == 2) {
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42 min <- min(result$coefficients[, 4][-1], na.rm = TRUE)
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43 lastname <- names(result$coefficients[, 4][-1])[result$coefficients[,4][-1] == min]
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44 }
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45 if (is.null(dim(d))) {
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46 d <- as.data.frame(d)
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47 colnames(d) <- lastname
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48 }
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49 lm1 <- glm(y ~ ., data = d, family=family, epsilon=epsilon)
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50 result <- summary(lm1)
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51 max <- max(result$coefficients[, 4][-1], na.rm = TRUE)
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52 if (length(result$coefficients[, 4][-1]) == 1) {
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53 max <- result$coefficients[, 4][-1]
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54 if (max > alfa) {
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55 max = 0
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56 lm1 <- glm(y ~ 1, family=family, epsilon=epsilon)
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57 }
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58 }
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59 }
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60 return(lm1)
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61 }
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62
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63 unlockBinding("stepback", as.environment("package:maSigPro"))
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64 assignInNamespace("stepback", stepback, ns="maSigPro", envir=as.environment("package:maSigPro"))
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65 assign("stepback", stepback, as.environment("package:maSigPro"))
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66 lockBinding("stepback", as.environment("package:maSigPro"))
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67 # End of temporary code to fix stepback.R
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68
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69 options(stringAsFactors = FALSE, useFancyQuotes = FALSE)
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70 args <- commandArgs(trailingOnly = TRUE)
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71
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72 # specify our desired options in a list
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73 # by default OptionParser will add an help option equivalent to
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74 # make_option(c("-h", "--help"), action="store_true", default=FALSE,
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75 # help="Show this help message and exit")
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76 option_list <- list(
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77 make_option(c("-q", "--quiet"), action="store_false",
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78 dest="verbose", help="Print little output"),
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79 make_option(c("-e", "--edesign"), type="character"),
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80 make_option(c("-d", "--data"), type="character"),
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81 make_option(c("-o", "--outfile"), type="character"),
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82 make_option("--degree", type="integer", default=1),
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83 make_option("--time_col", type="integer", default=1),
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84 make_option("--repl_col", type="integer", default=2),
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85 make_option("--qvalue", type="double", default=0.05),
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86 make_option("--min_obs", type="integer", default=6),
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87 make_option("--step_method", type="character", default="backward"),
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88 make_option("--nvar_correction", type="logical", default=FALSE),
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89 make_option("--alfa", type="double", default=0.05),
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90 make_option("--rsq", type="double", default=0.7),
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91 make_option("--vars", type="character", default="groups"),
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92 make_option("--significant_intercept", type="character", default="dummy"),
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93 make_option("--cluster_data", type="integer", default=1),
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94 make_option(c("-k", "--k"), type="integer", default=9),
2
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95 make_option("--print_cluster", type="logical", default=FALSE),
1
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96 make_option("--cluster_method", type="character", default="hclust"),
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97 make_option("--distance", type="character", default="cor"),
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98 make_option("--agglo_method", type="character", default="ward.D"),
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99 make_option("--iter_max", type="integer", default=500),
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100 make_option("--color_mode", type="character", default="rainbow"),
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101 make_option("--show_fit", type="logical", default=TRUE),
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102 make_option("--show_lines", type="logical", default=TRUE),
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103 make_option("--cexlab", type="double", default=0.8),
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104 make_option("--legend", type="logical", default=TRUE)
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105 )
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106
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107 # get command line options, if help option encountered print help and exit,
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108 # otherwise if options not found on command line then set defaults
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109 opt <- parse_args(OptionParser(option_list=option_list))
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110
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111 # enforce the following required arguments
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112 if (is.null(opt$edesign)) {
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113 cat("'edesign' is required\n")
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114 q(status=1)
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115 }
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116 if (is.null(opt$data)) {
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117 cat("'data' is required\n")
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118 q(status=1)
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119 }
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120 if (is.null(opt$outfile)) {
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121 cat("'outfile' is required\n")
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122 q(status=1)
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123 }
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124
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125 verbose <- if (is.null(opt$quiet)) {
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126 TRUE
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127 } else {
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128 FALSE
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129 }
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130
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131 edesign <- as.matrix(read.table(opt$edesign, header=TRUE, row.names = 1))
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132
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133 data <- read.table(opt$data, header=TRUE, check.names=FALSE)
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134
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135 results <- maSigPro(data, edesign, degree = opt$degree, time.col = opt$time_col,
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136 repl.col = opt$repl_col, Q = opt$qvalue, min.obs = opt$min_obs,
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137 step.method = opt$step_method, nvar.correction = opt$nvar_correction,
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138 alfa = opt$alfa, rsq = opt$rsq, vars = opt$vars,
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139 significant.intercept = opt$significant_intercept,
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140 cluster.data = opt$cluster_data, k = opt$k,
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141 cluster.method = opt$cluster_method, distance = opt$distance,
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142 agglo.method = opt$agglo_method, iter.max = opt$iter_max,
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143 color.mode = opt$color_mode, show.fit = opt$show_fit,
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144 show.lines = opt$show_lines, cexlab = opt$cexlab,
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145 legend = opt$legend)
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146
2
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147 if (opt$print_cluster) {
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148 for (i in 1:length(results$sig.genes)) {
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149
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150 colname <- paste(names(results$sig.genes)[i], "cluster", sep = "_")
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151
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152 results$summary[colname] <- ""
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153 results$summary[[colname]][1: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()