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annotate MetaRNASeq.R @ 38:c08b824e40cc draft

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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 86c0c3bb957558f14e9400171640bf5a5c6605c9
author sblanck
date Mon, 25 Jun 2018 05:25:40 -0400
parents a99bbda3cf1f
children 07ac07715f22
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1 #!/usr/bin/env Rscript
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2 # setup R error handling to go to stderr
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3 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
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5 # we need that to not crash galaxy with an UTF8 error on German LC settings.
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6 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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8 library("optparse")
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10 ##### Read options
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11 option_list=list(
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12 make_option("--input",type="character",default="NULL",help="list of rdata objects containing eset objects"),
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13 make_option("--inputName",type="character",default=NULL,help="filenames of the Rddata objects"),
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14 make_option("--nbreplicates",type="character",default=NULL,help="number of replicate per study"),
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15 make_option("--fdr",type="character",default=NULL,help="Adjusted p-value threshold to be declared differentially expressed"),
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16 make_option("--result",type="character",default=NULL,help="text file containing result of the meta-analysis"),
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17 make_option("--htmloutput",type="character",default=NULL,help="Output html report"),
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18 make_option("--htmloutputpath",type="character",default="NULL",help="Path of output html report"),
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19 make_option("--htmltemplate",type="character",default=NULL,help="html template)")
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20 );
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22 opt_parser = OptionParser(option_list=option_list);
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23 opt = parse_args(opt_parser);
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25 if(is.null(opt$input)){
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26 print_help(opt_parser)
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27 stop("input required.", call.=FALSE)
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28 }
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30 #loading libraries
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32 suppressPackageStartupMessages(require(affy))
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33 suppressPackageStartupMessages(require(annaffy))
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34 suppressPackageStartupMessages(require(VennDiagram))
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35 suppressPackageStartupMessages(require(GEOquery))
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37 listfiles <- trimws( unlist( strsplit(trimws(opt$input), ";") ) )
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38 listfilenames <- trimws( unlist( strsplit(trimws(opt$inputName), ";") ) )
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39 nbreplicates <- as.numeric(trimws( unlist( strsplit(trimws(opt$nbreplicates), ";") ) ))
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41 listfiles
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42 listfilenames
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43 nbreplicates
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47 #for (i in 1:length(listInput))
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48 #{
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49 # inputFileInfo <- unlist( strsplit( listInput[i], ';' ) )
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50 # listfiles=c(listfiles,inputFileInfo[1])
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51 # listfilenames=c(listfilenames,inputFileInfo[2])
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52 # nbreplicates[i]=as.numeric(inputFileInfo[3])
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53 #}
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56 outputfile <- opt$result
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57 result.html = opt$htmloutput
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58 html.files.path=opt$htmloutputpath
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59 result.template=opt$htmltemplate
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62 html.files.path
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64 alpha=as.numeric(opt$fdr)
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65
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66 listData=lapply(listfiles,read.table)
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67 orderData=lapply(listData, function(x) x[order(x[1]), ])
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68 rawpval=lapply(orderData,function(x) x[6])
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69 rawpval=lapply(rawpval, function(x) as.numeric(unlist(x)))
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70
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71 DE=list()
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72 DE=lapply(orderData, function(x) ifelse(x[7]<=0.05,1,0))
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73
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74 FC=list()
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75 FC=lapply(orderData, function(x) x[3])
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76
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77 DE=as.data.frame(DE)
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78 colnames(DE)=listfilenames
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79 FC=as.data.frame(FC)
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80 colnames(FC)=listfilenames
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81
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82 # combinations
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83 library(metaRNASeq)
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84 library(UpSetR)
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85 fishcomb<-fishercomb(rawpval, BHth=alpha)
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86 warning(length(rawpval))
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87 invnormcomb<-invnorm(rawpval, nrep=nbreplicates, BHth=alpha)
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88 #DE[["fishercomb"]]<-ifelse(fishcomb$adjpval<=alpha,1,0)
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89 #DE[["invnormcomb"]]<-ifelse(invnormcomb$adjpval<=alpha,1,0)
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90
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91 signsFC<-mapply(FC,FUN=function(x) sign(x))
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92 sumsigns<-apply(signsFC,1,sum)
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93 commonsgnFC<-ifelse(abs(sumsigns)==dim(signsFC)[2],sign(sumsigns),0)
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94
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95 DEresults <- data.frame(DE=DE,"DE.fishercomb"=ifelse(fishcomb$adjpval<=alpha,1,0),"DE.invnorm"=ifelse(invnormcomb$adjpval<=alpha,1,0))
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96
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97 unionDE <- unique(c(fishcomb$DEindices,invnormcomb$DEindices))
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98 FC.selecDE <- data.frame(DEresults[unionDE,],FC[unionDE,],signFC=commonsgnFC[unionDE])
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99 keepDE <- FC.selecDE[which(abs(FC.selecDE$signFC)==1),]
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100
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101 fishcomb_de <- rownames(keepDE)[which(keepDE[,"DE.fishercomb"]==1)]
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102 invnorm_de <- rownames(keepDE)[which(keepDE[,"DE.invnorm"]==1)]
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103 indstudy_de = list()
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104 for (i in 1:length(listfiles)) {
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105 currentIndstudy_de = rownames(keepDE)[which(keepDE[,i]==1)]
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106 indstudy_de[[listfilenames[i]]]=currentIndstudy_de
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107 }
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108
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109 IDDIRRfishcomb=IDD.IRR(fishcomb_de,indstudy_de)
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110 IDDIRRinvnorm=IDD.IRR(invnorm_de,indstudy_de)
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111
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112 conflits<-data.frame(ID=listData[[1]][rownames(DEresults),1],DE=DEresults,FC=FC,signFC=commonsgnFC)
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113 #write DE outputfile
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114 write.table(conflits, outputfile,sep="\t",,row.names=FALSE)
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115 library(VennDiagram)
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116 DE_num=apply(keepDE[,1:(length(listfiles)+2)], 2, FUN=function(x) which(x==1))
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117 #DE_num=apply(DEresults, 2, FUN=function(x) which(x==1))
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118 dir.create(html.files.path, showWarnings = TRUE, recursive = FALSE)
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119 temp.venn.plot = file.path( html.files.path, paste("venn.png"))
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120 if (length(listfiles)<=2) {
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121 title="VENN DIAGRAM"
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122 width=500
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123 venn.plot<-venn.diagram(x=as.list(DE_num),filename=NULL, col="black", fill=1:length(DE_num)+1,alpha=0.6)
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124 png(temp.venn.plot,width=width,height=500)
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125 grid.draw(venn.plot)
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126 dev.off()
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127 } else {
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128 title="UPSETR DIAGRAM"
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129 width=1000
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130 png(temp.venn.plot,width=width,height=500)
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131 upset(fromList(as.list(DE_num)), order.by = "freq")
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132 dev.off()
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133
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134 }
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135
2
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136
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137 library(jsonlite)
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138 matrixConflits=as.matrix(conflits)
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139 datajson=toJSON(matrixConflits,pretty = TRUE)
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140 summaryFishcombjson=toJSON(as.matrix(t(IDDIRRfishcomb)),pretty = TRUE)
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141 summaryinvnormjson=toJSON(as.matrix(t(IDDIRRinvnorm)),pretty = TRUE)
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142
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143 vennFilename="venn.png"
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144 vennFile=file.path(html.files.path,vennFilename)
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145 htmlfile=readChar(result.template, file.info(result.template)$size)
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146 htmlfile=gsub(x=htmlfile,pattern = "###DATAJSON###",replacement = datajson, fixed = TRUE)
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147 htmlfile=gsub(x=htmlfile,pattern = "###FISHSUMMARYJSON###",replacement = summaryFishcombjson, fixed = TRUE)
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148 htmlfile=gsub(x=htmlfile,pattern = "###INVSUMMARYJSON###",replacement = summaryinvnormjson, fixed = TRUE)
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149 htmlfile=gsub(x=htmlfile,pattern = "###VENN###",replacement = vennFilename, fixed = TRUE)
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150 htmlfile=gsub(x=htmlfile,pattern = "###WIDTH###",replacement = as.character(width), fixed = TRUE)
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151 htmlfile=gsub(x=htmlfile,pattern = "###TITLE###",replacement = title, fixed = TRUE)
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152 write(htmlfile,result.html)
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153