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annotate MetaRNASeq.R @ 4:58052f8bc987 draft

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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 8d4651e98155855108d1c4574392d503cc04bc95
author sblanck
date Thu, 01 Mar 2018 05:22:24 -0500
parents 1024245abc70
children 3ce32282f6a4
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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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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")
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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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)")
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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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)
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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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))
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32 suppressPackageStartupMessages(require(GEOquery))
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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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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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 }
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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46 outputfile <- opt$result
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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47 result.html = opt$htmloutput
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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48 html.files.path=opt$htmloutputpath
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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49 result.template=opt$htmltemplate
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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51 alpha=0.05
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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53 #print(comparison)
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 listData=lapply(listfiles,read.table)
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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56 orderData=lapply(listData, function(x) x[order(x[1]), ])
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57 rawpval=lapply(orderData,function(x) x[6])
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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58 rawpval=lapply(rawpval, function(x) as.numeric(unlist(x)))
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59
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60 DE=list()
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61 DE=lapply(orderData, function(x) ifelse(x[7]<=0.05,1,0))
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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63 FC=list()
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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64 FC=lapply(orderData, function(x) x[3])
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66 DE=as.data.frame(DE)
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67 colnames(DE)=listfilenames
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68 FC=as.data.frame(FC)
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69 colnames(FC)=listfilenames
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70 # the comparison must only have two values and the conds must
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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71 # be a vector from those values, at least one of each.
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73 #if (length(comparison) != 2) {
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74 # stop("Comparison type must be a tuple: ", cargs[length(cargs) - 8])
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75 #}
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77 sink("/dev/null")
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78 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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79 #library(DESeq)
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80 #library(HTSFilter)
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82 #DE=list()
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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83 #FC=list()
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84 #i=1
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86 # Open the html output file
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87 #file.conn = file(diag.html, open="w")
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88
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89 #writeLines( c("<html><body>"), file.conn)
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90
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91 # Perform deseq analysis on each study
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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92 #for(i in 1:length(listfiles))
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93 #{
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94 # f=listfiles[i]
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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95 # fname=listfilenames[i]
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96 # study_name=unlist(strsplit(fname,"[.]"))[1]
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97 # print(paste0("study.name ",study_name))
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98 # d <- read.table(f, sep=" ", header=TRUE, row.names=1)
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99 # conds<-sapply(strsplit(colnames(d),"[.]"),FUN=function(x) x[1])
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100 # if (length(unique(conds)) != 2) {
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101 # warning(as.data.frame(strsplit(colnames(d),"[.]")))
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102 # stop("You can only have two columns types: ", paste(conds,collapse=" "))
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103 # }
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104 # if (!identical(sort(comparison), sort(unique(conds)))) {
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105 # 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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106 # }
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107 # if (length(d) != length(conds)) {
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108 # 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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109 # }
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110 #
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111 # cds <- newCountDataSet(d, conds)
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112 # cds <- estimateSizeFactors(cds)
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113 #
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114 # cdsBlind <- estimateDispersions( cds, method="blind" )
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115 #
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116 # if (length(conds) != 2) {
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117 # cds <- estimateDispersions( cds )
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118 # norep = FALSE
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119 # }
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120 #
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121 # if (length(conds) == 2) {
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122 # cds <- estimateDispersions( cds, method=method, sharingMode=mod, fitType="parametric" )
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123 # norep = TRUE
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124 # }
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125 #
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126 # filter<-HTSFilter(cds, plot=FALSE)
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127 # cds.filter<-filter$filteredData
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128 # on.index<-which(filter$on==1)
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129 #
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130 # res<-as.data.frame(matrix(NA,nrow=nrow(cds),ncol=ncol(cds)))
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131 # nbT <- nbinomTest(cds.filter, comparison[1], comparison[2])
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132 # colnames(res)<-colnames(nbT)
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133 # res[on.index,]<-nbT
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134 # #write.table(res[order(res$padj), ], file=outputfile, quote=FALSE, row.names=FALSE, sep="\t")
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135 #
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136 #
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137 # temp.pval.plot = file.path( html.files.path, paste("PvalHist",i,".png",sep=""))
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138 # png( temp.pval.plot, width=500, height=500 )
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139 # hist(res$pval, breaks=100, col="skyblue", border="slateblue", main="")
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140 # dev.off()
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141 #
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142 # writeLines( c("<h2>P-value histogram for ",study_name,"</h2>"), file.conn)
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143 # writeLines( c("<img src='PvalHist",i,".png'><br/><br/>"), file.conn)
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144 #
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145 # #on enregistre la p-value
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146 # rawpval[[study_name]]<-res$pval
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147 # DE[[study_name]]<-ifelse(res$padj<=alpha,1,0)
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148 # FC[[study_name]]<-res$log2FoldChange
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149 #
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150 # i=i+1
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151 #}
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152
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153
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154 # combinations
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155 library(metaRNASeq)
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156 fishcomb<-fishercomb(rawpval, BHth=alpha)
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157 warning(length(rawpval))
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158 invnormcomb<-invnorm(rawpval, nrep=c(8,8), BHth=alpha)
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159 #DE[["fishercomb"]]<-ifelse(fishcomb$adjpval<=alpha,1,0)
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160 #DE[["invnormcomb"]]<-ifelse(invnormcomb$adjpval<=alpha,1,0)
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161
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162 signsFC<-mapply(FC,FUN=function(x) sign(x))
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163 sumsigns<-apply(signsFC,1,sum)
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164 commonsgnFC<-ifelse(abs(sumsigns)==dim(signsFC)[2],sign(sumsigns),0)
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165
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166 DEresults <- data.frame(DE=DE,"DE.fishercomb"=ifelse(fishcomb$adjpval<=alpha,1,0),"DE.invnorm"=ifelse(invnormcomb$adjpval<=alpha,1,0))
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167
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168 unionDE <- unique(c(fishcomb$DEindices,invnormcomb$DEindices))
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169 FC.selecDE <- data.frame(DEresults[unionDE,],FC[unionDE,],signFC=commonsgnFC[unionDE])
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170 keepDE <- FC.selecDE[which(abs(FC.selecDE$signFC)==1),]
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171
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172 fishcomb_de <- rownames(keepDE)[which(keepDE[,"DE.fishercomb"]==1)]
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173 invnorm_de <- rownames(keepDE)[which(keepDE[,"DE.invnorm"]==1)]
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174 indstudy_de = list()
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175 for (i in 1:length(listfiles)) {
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176 currentIndstudy_de = rownames(keepDE)[which(keepDE[,i]==1)]
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177 indstudy_de[[listfilenames[i]]]=currentIndstudy_de
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178 }
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179
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180 IDDIRRfishcomb=IDD.IRR(fishcomb_de,indstudy_de)
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181 IDDIRRinvnorm=IDD.IRR(invnorm_de,indstudy_de)
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182
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183 #conflits<-data.frame(ID=listData[[1]][rownames(DEresults),1],Fishercomb=DEresults[["DE.fishercomb"]],Invnormcomb=DEresults[["DE.invnorm"]],sign=commonsgnFC)
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184 conflits<-data.frame(ID=listData[[1]][rownames(DEresults),1],DE=DEresults,FC=FC,signFC=commonsgnFC)
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185 #write DE outputfile
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186 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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187 library(VennDiagram)
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188 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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189 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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190 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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191 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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192 grid.draw(venn.plot)
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193 dev.off()
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194
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195 library(jsonlite)
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196 matrixConflits=as.matrix(conflits)
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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197 datajson=toJSON(matrixConflits,pretty = TRUE)
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198 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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199 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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200
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201
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202 #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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203 #venn=paste0("./",vennsplit[length(vennsplit)])
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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204
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205
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206 vennFilename="venn.png"
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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207 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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208 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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209 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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210 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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211 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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212 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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213 write(htmlfile,result.html)
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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214
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215 #library(VennDiagram)
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216 #flog.threshold(ERROR)
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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217 #
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218 ##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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219 #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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220 #
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221 #showVenn<-function(liste,file)
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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222 #{
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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223 # 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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224 # filename = vennFilename, col = "black",
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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225 # 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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226 # 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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227 ## png(file);
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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228 ## grid.draw(venn.plot);
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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229 ## dev.off();
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230 #
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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231 #}
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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232 #
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233 #l=list()
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234 #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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235 #{
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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236 # 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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237 #}
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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238 #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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239 #showVenn(l,vennFile)
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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240 #file.copy(vennFilename,result.path)
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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
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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243 #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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244 #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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245 #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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246 #close(file.conn)
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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247 #print("passe6")
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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248 #sink(NULL)