Mercurial > repos > blankenberglab > gpca

annotate r-gpca.R @ 2:4865e7f4e9c5 draft

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planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit b72f398663cc133523cae0f5d7db2af1b4312f7a
author blankenberglab
date Tue, 27 Nov 2018 12:29:58 -0500
parents d93629e79f5e
children 8def7dda3bee
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0
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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1 #!/usr/bin/env Rscript
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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2 library(optparse)
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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3 library(gPCA)
1
d93629e79f5e planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit 3b791d44853d8928046914cd93112bdcf89d4965
blankenberglab
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4 options(bitmapType='cairo')
0
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5
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6
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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7 # parse options
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8 option_list = list(
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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9 make_option(
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10 c("--version"),
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blankenberglab
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11 action = "store_true",
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12 default = FALSE,
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blankenberglab
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13 help = "Print version and exit"
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14 ),
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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15 make_option(
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16 c("-i", "--batch"),
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blankenberglab
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17 action = "store",
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18 default = NA,
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19 type = 'character',
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blankenberglab
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20 help = "Input batch"
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21 ),
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22 make_option(
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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23 c("-d", "--data"),
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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24 action = "store",
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
blankenberglab
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25 default = NA,
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26 type = 'character',
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27 help = "Input data"
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28 ),
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29 make_option(
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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30 c("-n", "--nperm"),
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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31 action = "store",
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32 default = 1000,
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33 type = 'numeric',
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34 help = "Number of permutations to preform"
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35 ),
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36 make_option(
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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37 c("-c", "--center"),
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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38 action = "store_true",
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39 default = FALSE,
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blankenberglab
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40 help = "Is the input batch and data centered [default %default]"
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41 ),
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42 make_option(
ed24bacaa4d0 planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty
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43 c("-y", "--scaleY"),
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44 action = "store_true",
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45 default = FALSE,
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46 help = "Scale to Y axis"
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47 ),
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48 make_option(
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49 c("-f", "--filt"),
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50 action = "store",
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51 default = NULL,
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52 type = 'numeric',
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53 help = "Retain features"
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54 ),
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55 make_option(
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56 c( "--npcs"),
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57 action = "store",
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58 default = 3,
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59 type = 'numeric',
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60 help = "Number of principal components to plot"
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61 ),
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62 make_option(
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63 c("-p", "--path"),
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64 action = "store",
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65 default = '$html_outfile.extra_files_path',
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66 type = 'character',
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67 help = "File path"
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68 ),
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69 make_option(
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70 c("-s", "--seed"),
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71 action = "store",
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72 default = NULL,
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73 type = 'numeric',
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74 help = "Set a seed number"
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75 ),
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76 make_option(
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77 c("-x", "--numbers_outfile"),
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78 action = "store",
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79 default = NA,
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80 type = 'character',
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81 help = "Numbers output"
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82 ),
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83 make_option(
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84 c("-o", "--html_outfile"),
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85 action = "store",
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86 default = NA,
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87 type = 'character',
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88 help = "Output",
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89 )
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90 )
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91
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92 opt <-parse_args(OptionParser(option_list = option_list))
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93
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94 if (opt$version){
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95 # print version and exit
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96 cat(paste("gPCA version", toString(packageVersion("gPCA"))), "\n")
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97 quit()
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98 }
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99
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100 # Check parameter values
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101
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102 if ( ! file.exists(opt$batch)){
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103 stop((paste('File for batch', opt$batch, 'does not exist')))
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104 }
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105 if ( ! file.exists(opt$data)){
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106 stop((paste('File for data', opt$data, 'does not exist')))
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107 }
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108
1
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109 dir.create(opt$path);
0
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110 data<-t(as.matrix(read.delim(opt$data, row.names=1, header=TRUE, sep="\t")))
1
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111 batch<-as.matrix(read.delim(opt$batch, header=TRUE, row.names=1, sep="\t"))
0
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112
1
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113 write('#Batch\tDelta\tP-value\tCumulative Variance',file = opt$numbers_outfile, append=TRUE)
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114
2
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115 write('<html><body><div align="left" id="top"><p><h1>Table of Contents</h1><ul>',file = opt$html_outfile, append=TRUE)
1
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116 for (row in 1:nrow(batch)) {
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117 write(paste0('<li><a href="#',row.names(batch)[row],'">',row.names(batch)[row],'</a></li>'), file=opt$html_outfile, append=TRUE)
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118 }
2
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119 write('</ul></p></div>', file=opt$html_outfile, append=TRUE)
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120
1
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121 for (row in 1:nrow(batch)) {
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122 batch1<-as.numeric(factor(batch[row,]))
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123
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124 out<-gPCA.batchdetect(x=data, batch=batch1, center=opt$center, scaleY=opt$scaleY, nperm=opt$nperm, filt=opt$filt, seed=opt$seed)
0
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125
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126 out$varPCg1<-((out$varPCg1-out$varPCu1)/out$varPCg1)*100
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127
1
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128 write(paste(row.names(batch)[row],out$delta,out$p.val,out$varPCg1,sep="\t"),file = opt$numbers_outfile, append=TRUE)
0
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129
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130 # General Distribution
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131 par(mai=c(0.8,0.8,0.1,0.1),cex=0.8)
1
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132 png(paste(opt$path,'/gDist_',row,'.png', sep=""), width=1020, height=800, units='px')
0
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133 gDist(out)
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134 invisible(dev.off())
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135
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136
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137 # Guided/Unguided 1v2
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138 par(mai=c(0.8,0.8,0.1,0.1),cex=0.8)
1
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139 png(paste(opt$path,'/guided_1v2_',row,'.png', sep=""), width=1020, height=800, units='px')
0
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140 PCplot(out,ug="unguided",type="1v2")
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141 invisible(dev.off())
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142
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143 par(mai=c(0.8,0.8,0.1,0.1),cex=0.8)
1
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144 png(paste(opt$path,'/unguided_1v2_',row,'.png', sep=""), width=1020, height=800, units='px')
0
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145 PCplot(out,ug="unguided",type="1v2")
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146 invisible(dev.off())
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147
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148
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149 # Guided/Unguided comp,3
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150 par(mai=c(0.65,0.65,0.1,0.1),cex=0.8)
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151 png(paste(opt$path,'/guided_npcs_',row,'.png', sep=""), width=1020, height=800, units='px')
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152 PCplot(out,ug="guided",type="comp",npcs=opt$npcs)
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153 invisible(dev.off())
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154
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155 par(mai=c(0.65,0.65,0.1,0.1),cex=0.8)
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156 png(paste(opt$path,'/unguided_npcs_',row,'.png', sep=""), width=1020, height=800, units='px')
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157 PCplot(out,ug="unguided",type="comp",npcs=opt$npcs)
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158 invisible(dev.off())
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159
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160
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161 # Guided/Unguided CumlativeVarPlot
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162 par(mai=c(0.8,0.8,0.1,0.1),cex=0.8)
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163 png(paste(opt$path,'/guided_var_',row,'.png', sep=""), width=1020, height=800, units='px')
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164 CumulativeVarPlot(out,ug="guided",col="blue")
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165 invisible(dev.off())
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166
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167 par(mai=c(0.8,0.8,0.1,0.1),cex=0.8)
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168 png(paste(opt$path,'/unguided_var_',row,'.png', sep=""), width=1020, height=800, units='px')
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169 CumulativeVarPlot(out,ug="unguided",col="blue")
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170 invisible(dev.off())
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171
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172
1
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173 write(paste0('
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174 <header id=',row.names(batch)[row],'><center><font size="11">',row.names(batch)[row],'</font><center></header>
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175 <br>
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176 <table align="center" border="1">
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177 <tr>
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178 <th>Delta</th><th>P-value</th><th>varPCg1</th>
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179 </tr>
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180 <tr>
1
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181 <td id="#">',out$delta,'</td><td id=p.val>',out$p.val,'</td><td id=varPCg1>',out$varPCg1,'</td>
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182 </tr>
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183 </table>
1
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184 <center><img src="gDist_',row,'.png"/></center><br>
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185 <center><title>Guided 1v2</title><br><img src="guided_1v2_',row,'.png"/></center><br>
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186 <center><title>Unguided 1v2</title><br><img src="unguided_1v2_',row,'.png"/></center><br>
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187
1
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188 <center><title>Guided Compare to ',opt$npcs,'</title><br><img src="guided_npcs_',row,'.png"/></center><br>
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189 <center><title>Unguided Compare to ',opt$npcs,'</title><br><img src="unguided_npcs_',row,'.png"/></center><br>
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190
1
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191 <center><title>Guided Cumulative Variance</title><br><img src="guided_var_',row,'.png"/></center><br>
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192 <center><title>Unguided Cumulative Variance</title><br><img src="unguided_var_',row,'.png"/></center><br>
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193
1
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194 '), file = opt$html_outfile, append=TRUE)
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195 }
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196 write(paste('<p><center><a href="#top">Back to Top</a></center></p></body></html>'),file = opt$html_outfile, append=TRUE)
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197
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198 sessionInfo()