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annotate MetaRNASeq.R @ 0:1024245abc70 draft

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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
author sblanck
date Thu, 22 Feb 2018 08:38:22 -0500
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children 58052f8bc987
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1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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1 #!/usr/bin/env Rscript
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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2 # setup R error handling to go to stderr
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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3 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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5 # we need that to not crash galaxy with an UTF8 error on German LC settings.
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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6 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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8 library("optparse")
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10 ##### Read options
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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11 option_list=list(
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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12 make_option("--input",type="character",default="NULL",help="list of rdata objects containing eset objects"),
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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13 make_option("--result",type="character",default=NULL,help="text file containing result of the meta-analysis"),
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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14 make_option("--htmloutput",type="character",default=NULL,help="Output html report"),
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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15 make_option("--htmloutputpath",type="character",default="NULL",help="Path of output html report"),
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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16 make_option("--htmltemplate",type="character",default=NULL,help="html template)")
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17 );
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19 opt_parser = OptionParser(option_list=option_list);
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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20 opt = parse_args(opt_parser);
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22 if(is.null(opt$input)){
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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23 print_help(opt_parser)
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24 stop("input required.", call.=FALSE)
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25 }
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1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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27 #loading libraries
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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29 suppressPackageStartupMessages(require(affy))
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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30 suppressPackageStartupMessages(require(annaffy))
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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31 suppressPackageStartupMessages(require(VennDiagram))
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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32 suppressPackageStartupMessages(require(GEOquery))
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34 listInput <- trimws( unlist( strsplit(trimws(opt$input), ",") ) )
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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36 listfiles=vector()
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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37 listfilenames=vector()
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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38
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39 for (i in 1:length(listInput))
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40 {
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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41 inputFileInfo <- unlist( strsplit( listInput[i], ';' ) )
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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42 listfiles=c(listfiles,inputFileInfo[1])
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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43 listfilenames=c(listfilenames,inputFileInfo[2])
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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44 }
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46 cargs <- commandArgs()
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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47 cargs <- cargs[(which(cargs == "--args")+1):length(cargs)]
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48 nbargs=length(cargs)
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49 listfiles=vector()
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50 listfilenames=vector()
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51 for (i in seq(1,nbargs-6,2)) {
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52 listfiles=c(listfiles,cargs[[i]])
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53 listfilenames=c(listfilenames,cargs[[i+1]])
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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54 }
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55 #mod<-cargs[[length(cargs) - 6]]
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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
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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60
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61 alpha=0.05
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63 #print(comparison)
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64
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65 listData=lapply(listfiles,read.table)
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66 orderData=lapply(listData, function(x) x[order(x[1]), ])
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67 rawpval=lapply(orderData,function(x) x[6])
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68 rawpval=lapply(rawpval, function(x) as.numeric(unlist(x)))
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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70 DE=list()
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71 DE=lapply(orderData, function(x) ifelse(x[7]<=0.05,1,0))
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72
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73 FC=list()
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74 FC=lapply(orderData, function(x) x[3])
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76 DE=as.data.frame(DE)
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77 colnames(DE)=listfilenames
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78 FC=as.data.frame(FC)
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79 colnames(FC)=listfilenames
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80 # the comparison must only have two values and the conds must
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81 # be a vector from those values, at least one of each.
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82
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83 #if (length(comparison) != 2) {
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84 # stop("Comparison type must be a tuple: ", cargs[length(cargs) - 8])
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85 #}
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86
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87 sink("/dev/null")
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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88 dir.create(html.files.path, recursive=TRUE)
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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89 #library(DESeq)
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90 #library(HTSFilter)
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91
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92 #DE=list()
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93 #FC=list()
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94 #i=1
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95
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96 # Open the html output file
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97 #file.conn = file(diag.html, open="w")
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98
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99 #writeLines( c("<html><body>"), file.conn)
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100
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101 # Perform deseq analysis on each study
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102 #for(i in 1:length(listfiles))
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103 #{
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104 # f=listfiles[i]
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105 # fname=listfilenames[i]
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106 # study_name=unlist(strsplit(fname,"[.]"))[1]
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107 # print(paste0("study.name ",study_name))
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108 # d <- read.table(f, sep=" ", header=TRUE, row.names=1)
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109 # conds<-sapply(strsplit(colnames(d),"[.]"),FUN=function(x) x[1])
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110 # if (length(unique(conds)) != 2) {
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111 # warning(as.data.frame(strsplit(colnames(d),"[.]")))
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112 # stop("You can only have two columns types: ", paste(conds,collapse=" "))
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113 # }
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114 # if (!identical(sort(comparison), sort(unique(conds)))) {
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115 # stop("Column types must use the two names from Comparison type, and vice versa. Must have at least one of each in the Column types.\nColumn types: ", cargs[2], "\n", "Comparison type: ", cargs[3])
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116 # }
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117 # if (length(d) != length(conds)) {
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118 # stop("Number of total sample columns in counts file must correspond to the columns types field. E.g. if column types is 'kidney,kidney,liver,liver' then number of sample columns in counts file must be 4 as well.")
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119 # }
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120 #
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121 # cds <- newCountDataSet(d, conds)
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122 # cds <- estimateSizeFactors(cds)
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123 #
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124 # cdsBlind <- estimateDispersions( cds, method="blind" )
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125 #
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126 # if (length(conds) != 2) {
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127 # cds <- estimateDispersions( cds )
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128 # norep = FALSE
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129 # }
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130 #
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131 # if (length(conds) == 2) {
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132 # cds <- estimateDispersions( cds, method=method, sharingMode=mod, fitType="parametric" )
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133 # norep = TRUE
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134 # }
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135 #
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136 # filter<-HTSFilter(cds, plot=FALSE)
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137 # cds.filter<-filter$filteredData
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138 # on.index<-which(filter$on==1)
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139 #
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140 # res<-as.data.frame(matrix(NA,nrow=nrow(cds),ncol=ncol(cds)))
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141 # nbT <- nbinomTest(cds.filter, comparison[1], comparison[2])
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142 # colnames(res)<-colnames(nbT)
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143 # res[on.index,]<-nbT
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144 # #write.table(res[order(res$padj), ], file=outputfile, quote=FALSE, row.names=FALSE, sep="\t")
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145 #
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146 #
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147 # temp.pval.plot = file.path( html.files.path, paste("PvalHist",i,".png",sep=""))
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148 # png( temp.pval.plot, width=500, height=500 )
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149 # hist(res$pval, breaks=100, col="skyblue", border="slateblue", main="")
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150 # dev.off()
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151 #
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152 # writeLines( c("<h2>P-value histogram for ",study_name,"</h2>"), file.conn)
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153 # writeLines( c("<img src='PvalHist",i,".png'><br/><br/>"), file.conn)
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154 #
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155 # #on enregistre la p-value
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156 # rawpval[[study_name]]<-res$pval
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157 # DE[[study_name]]<-ifelse(res$padj<=alpha,1,0)
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158 # FC[[study_name]]<-res$log2FoldChange
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159 #
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160 # i=i+1
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161 #}
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162
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163
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164 # combinations
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165 library(metaRNASeq)
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166 fishcomb<-fishercomb(rawpval, BHth=alpha)
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167 warning(length(rawpval))
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168 invnormcomb<-invnorm(rawpval, nrep=c(8,8), BHth=alpha)
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169 #DE[["fishercomb"]]<-ifelse(fishcomb$adjpval<=alpha,1,0)
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170 #DE[["invnormcomb"]]<-ifelse(invnormcomb$adjpval<=alpha,1,0)
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171
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172 signsFC<-mapply(FC,FUN=function(x) sign(x))
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173 sumsigns<-apply(signsFC,1,sum)
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174 commonsgnFC<-ifelse(abs(sumsigns)==dim(signsFC)[2],sign(sumsigns),0)
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175
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176 DEresults <- data.frame(DE=DE,"DE.fishercomb"=ifelse(fishcomb$adjpval<=alpha,1,0),"DE.invnorm"=ifelse(invnormcomb$adjpval<=alpha,1,0))
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177
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178 unionDE <- unique(c(fishcomb$DEindices,invnormcomb$DEindices))
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179 FC.selecDE <- data.frame(DEresults[unionDE,],FC[unionDE,],signFC=commonsgnFC[unionDE])
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180 keepDE <- FC.selecDE[which(abs(FC.selecDE$signFC)==1),]
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181
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182 fishcomb_de <- rownames(keepDE)[which(keepDE[,"DE.fishercomb"]==1)]
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183 invnorm_de <- rownames(keepDE)[which(keepDE[,"DE.invnorm"]==1)]
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184 indstudy_de = list()
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185 for (i in 1:length(listfiles)) {
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186 currentIndstudy_de = rownames(keepDE)[which(keepDE[,i]==1)]
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187 indstudy_de[[listfilenames[i]]]=currentIndstudy_de
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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188 }
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189
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190 IDDIRRfishcomb=IDD.IRR(fishcomb_de,indstudy_de)
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191 IDDIRRinvnorm=IDD.IRR(invnorm_de,indstudy_de)
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192
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193 #conflits<-data.frame(ID=listData[[1]][rownames(DEresults),1],Fishercomb=DEresults[["DE.fishercomb"]],Invnormcomb=DEresults[["DE.invnorm"]],sign=commonsgnFC)
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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194 conflits<-data.frame(ID=listData[[1]][rownames(DEresults),1],DE=DEresults,FC=FC,signFC=commonsgnFC)
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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195 #write DE outputfile
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196 write.table(conflits, outputfile,sep="\t",,row.names=FALSE)
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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197 library(VennDiagram)
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198 DE_num=apply(DEresults, 2, FUN=function(x) which(x==1))
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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199 venn.plot<-venn.diagram(x=as.list(DE_num),filename=NULL, col="black", fill=1:length(DE_num)+1,alpha=0.6)
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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200 temp.venn.plot = file.path( html.files.path, paste("venn.png"))
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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201 png(temp.venn.plot,width=500,height=500)
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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202 grid.draw(venn.plot)
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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203 dev.off()
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204
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205 library(jsonlite)
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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206 matrixConflits=as.matrix(conflits)
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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207 datajson=toJSON(matrixConflits,pretty = TRUE)
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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208 summaryFishcombjson=toJSON(as.matrix(t(IDDIRRfishcomb)),pretty = TRUE)
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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209 summaryinvnormjson=toJSON(as.matrix(t(IDDIRRinvnorm)),pretty = TRUE)
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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210
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211
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212 #vennsplit=strsplit(result.venn,split="/")[[1]]
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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213 #venn=paste0("./",vennsplit[length(vennsplit)])
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214
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215
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216 vennFilename="venn.png"
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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217 vennFile=file.path(html.files.path,vennFilename)
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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218 htmlfile=readChar(result.template, file.info(result.template)$size)
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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219 htmlfile=gsub(x=htmlfile,pattern = "###DATAJSON###",replacement = datajson, fixed = TRUE)
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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220 htmlfile=gsub(x=htmlfile,pattern = "###FISHSUMMARYJSON###",replacement = summaryFishcombjson, fixed = TRUE)
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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221 htmlfile=gsub(x=htmlfile,pattern = "###INVSUMMARYJSON###",replacement = summaryinvnormjson, fixed = TRUE)
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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222 htmlfile=gsub(x=htmlfile,pattern = "###VENN###",replacement = vennFilename, fixed = TRUE)
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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223 write(htmlfile,result.html)
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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224
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225 #library(VennDiagram)
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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226 #flog.threshold(ERROR)
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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227 #
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228 ##venn.plot<-venn.diagram(x = c(res[c(1:(length(res)-3))],meta=list(res$Meta)),filename = v, col = "black", fill = c(1:(length(res)-2)), margin=0.05, alpha = 0.6,imagetype = "png")
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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229 #dir.create(result.path, showWarnings = TRUE, recursive = FALSE)
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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230 #
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231 #showVenn<-function(liste,file)
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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232 #{
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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233 # venn.plot<-venn.diagram(x = liste,
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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234 # filename = vennFilename, col = "black",
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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235 # fill = 1:length(liste)+1,
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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236 # margin=0.05, alpha = 0.6,imagetype = "png")
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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237 ## png(file);
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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238 ## grid.draw(venn.plot);
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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239 ## dev.off();
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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240 #
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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241 #}
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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242 #
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243 #l=list()
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244 #for(i in 1:length(esets))
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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245 #{
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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246 # l[[paste("study",i,sep="")]]<-res[[i]]
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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247 #}
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248 #l[["Meta"]]=res[[length(res)-1]]
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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249 #showVenn(l,vennFile)
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250 #file.copy(vennFilename,result.path)
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251
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252
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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253 #writeLines( c("<h2>Venn Plot</h2>"), file.conn)
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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254 #writeLines( c("<img src='venn.png'><br/><br/>"), file.conn)
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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255 #writeLines( c("</body></html>"), file.conn)
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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256 #close(file.conn)
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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257 #print("passe6")
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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258 #sink(NULL)