smagexp: MetaMA.R annotate

annotate MetaMA.R @ 21:f953fdee364c draft

planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit ecb5d3451f1623e0cc649ac5197e66995ce19eef-dirty

author	sblanck
date	Thu, 22 Feb 2018 10:19:47 -0500
parents	a4015af2ae12
children	22e1325aaa88

rev	line source
9 328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 2 diff changeset	1 #!/usr/bin/env Rscript
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 2 diff changeset	2 # setup R error handling to go to stderr
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 2 diff changeset	3 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 2 diff changeset	4
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 2 diff changeset	5 # we need that to not crash galaxy with an UTF8 error on German LC settings.
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 2 diff changeset	6 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 2 diff changeset	7
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 2 diff changeset	8 library("optparse")
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 2 diff changeset	9
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 2 diff changeset	10 ##### Read options
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 2 diff changeset	11 option_list=list(
20 a4015af2ae12 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit a25677963b28019d4434bbe411b28168c912d71d sblanck parents: 10 diff changeset	12 make_option("--input",type="character",default="NULL",help="List of rdata objects containing eset objects"),
a4015af2ae12 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit a25677963b28019d4434bbe411b28168c912d71d sblanck parents: 10 diff changeset	13 make_option("--species",type="character",default="NULL",help="Species for annotations"),
9 328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 2 diff changeset	14 make_option("--htmloutput",type="character",default=NULL,help="Output html report"),
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 2 diff changeset	15 make_option("--htmloutputpath",type="character",default="NULL",help="Path of output html report"),
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 2 diff changeset	16 make_option("--htmltemplate",type="character",default=NULL,help="html template)")
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 2 diff changeset	17 );
2 93451f832736 Uploaded sblanck parents: diff changeset	18
9 328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 2 diff changeset	19 opt_parser = OptionParser(option_list=option_list);
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 2 diff changeset	20 opt = parse_args(opt_parser);
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 2 diff changeset	21
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 2 diff changeset	22 if(is.null(opt$input)){
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 2 diff changeset	23 print_help(opt_parser)
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 2 diff changeset	24 stop("input required.", call.=FALSE)
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 2 diff changeset	25 }
20 a4015af2ae12 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit a25677963b28019d4434bbe411b28168c912d71d sblanck parents: 10 diff changeset	26 if(is.null(opt$species)){
a4015af2ae12 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit a25677963b28019d4434bbe411b28168c912d71d sblanck parents: 10 diff changeset	27 print_help(opt_parser)
a4015af2ae12 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit a25677963b28019d4434bbe411b28168c912d71d sblanck parents: 10 diff changeset	28 stop("input required.", call.=FALSE)
a4015af2ae12 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit a25677963b28019d4434bbe411b28168c912d71d sblanck parents: 10 diff changeset	29 }
2 93451f832736 Uploaded sblanck parents: diff changeset	30
9 328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 2 diff changeset	31 #loading libraries
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 2 diff changeset	32
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 2 diff changeset	33 suppressPackageStartupMessages(require(metaMA))
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 2 diff changeset	34 suppressPackageStartupMessages(require(affy))
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 2 diff changeset	35 suppressPackageStartupMessages(require(annaffy))
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 2 diff changeset	36 suppressPackageStartupMessages(require(VennDiagram))
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 2 diff changeset	37 suppressPackageStartupMessages(require(GEOquery))
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 2 diff changeset	38
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 2 diff changeset	39 listInput <- trimws( unlist( strsplit(trimws(opt$input), ",") ) )
20 a4015af2ae12 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit a25677963b28019d4434bbe411b28168c912d71d sblanck parents: 10 diff changeset	40 species=opt$species
9 328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 2 diff changeset	41
2 93451f832736 Uploaded sblanck parents: diff changeset	42 rdataList=list()
93451f832736 Uploaded sblanck parents: diff changeset	43 condition1List=list()
93451f832736 Uploaded sblanck parents: diff changeset	44 condition2List=list()
9 328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 2 diff changeset	45 for (input in listInput)
2 93451f832736 Uploaded sblanck parents: diff changeset	46 {
9 328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 2 diff changeset	47 load(input)
2 93451f832736 Uploaded sblanck parents: diff changeset	48
93451f832736 Uploaded sblanck parents: diff changeset	49 rdataList=c(rdataList,(eset))
93451f832736 Uploaded sblanck parents: diff changeset	50 condition1List=c(condition1List,saveConditions[1])
93451f832736 Uploaded sblanck parents: diff changeset	51 condition2List=c(condition2List,saveConditions[2])
93451f832736 Uploaded sblanck parents: diff changeset	52
93451f832736 Uploaded sblanck parents: diff changeset	53 }
93451f832736 Uploaded sblanck parents: diff changeset	54
10 56267e3293b2 planemo upload commit 0ad899de37d891f387912b7abd63506605a25976-dirty sblanck parents: 9 diff changeset	55 result.html<-opt$htmloutput
56267e3293b2 planemo upload commit 0ad899de37d891f387912b7abd63506605a25976-dirty sblanck parents: 9 diff changeset	56 result.path<-opt$htmloutputpath
56267e3293b2 planemo upload commit 0ad899de37d891f387912b7abd63506605a25976-dirty sblanck parents: 9 diff changeset	57 result.template<-opt$htmltemplate
2 93451f832736 Uploaded sblanck parents: diff changeset	58
93451f832736 Uploaded sblanck parents: diff changeset	59 showVenn<-function(res,file)
93451f832736 Uploaded sblanck parents: diff changeset	60 {
93451f832736 Uploaded sblanck parents: diff changeset	61 venn.plot<-venn.diagram(x = c(res[c(1:(length(res)-3))],meta=list(res$Meta)),
93451f832736 Uploaded sblanck parents: diff changeset	62 filename = NULL, col = "black",
93451f832736 Uploaded sblanck parents: diff changeset	63 fill = c(1:(length(res)-2)),
93451f832736 Uploaded sblanck parents: diff changeset	64 margin=0.05, alpha = 0.6)
93451f832736 Uploaded sblanck parents: diff changeset	65 jpeg(file)
93451f832736 Uploaded sblanck parents: diff changeset	66 grid.draw(venn.plot)
93451f832736 Uploaded sblanck parents: diff changeset	67 dev.off()
93451f832736 Uploaded sblanck parents: diff changeset	68 }
93451f832736 Uploaded sblanck parents: diff changeset	69
20 a4015af2ae12 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit a25677963b28019d4434bbe411b28168c912d71d sblanck parents: 10 diff changeset	70 if(!species %in% installed.packages()[,"Package"]) {
a4015af2ae12 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit a25677963b28019d4434bbe411b28168c912d71d sblanck parents: 10 diff changeset	71 source("https://bioconductor.org/biocLite.R")
a4015af2ae12 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit a25677963b28019d4434bbe411b28168c912d71d sblanck parents: 10 diff changeset	72 biocLite(species)
a4015af2ae12 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit a25677963b28019d4434bbe411b28168c912d71d sblanck parents: 10 diff changeset	73 }
a4015af2ae12 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit a25677963b28019d4434bbe411b28168c912d71d sblanck parents: 10 diff changeset	74
21 f953fdee364c planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit ecb5d3451f1623e0cc649ac5197e66995ce19eef-dirty sblanck parents: 20 diff changeset	75 library("org.Hs.eg.db")
2 93451f832736 Uploaded sblanck parents: diff changeset	76 x <- org.Hs.egUNIGENE
93451f832736 Uploaded sblanck parents: diff changeset	77 mapped_genes <- mappedkeys(x)
93451f832736 Uploaded sblanck parents: diff changeset	78 link <- as.list(x[mapped_genes])
93451f832736 Uploaded sblanck parents: diff changeset	79
93451f832736 Uploaded sblanck parents: diff changeset	80 probe2unigene<-function(expset){
93451f832736 Uploaded sblanck parents: diff changeset	81 #construction of the map probe->unigene
93451f832736 Uploaded sblanck parents: diff changeset	82 probes=rownames(exprs(expset))
93451f832736 Uploaded sblanck parents: diff changeset	83 gene_id=fData(expset)[probes,"ENTREZ_GENE_ID"]
93451f832736 Uploaded sblanck parents: diff changeset	84 unigene=link[gene_id]
93451f832736 Uploaded sblanck parents: diff changeset	85 names(unigene)<-probes
93451f832736 Uploaded sblanck parents: diff changeset	86 probe_unigene=unigene
93451f832736 Uploaded sblanck parents: diff changeset	87 }
93451f832736 Uploaded sblanck parents: diff changeset	88
93451f832736 Uploaded sblanck parents: diff changeset	89 unigene2probe<-function(map)
93451f832736 Uploaded sblanck parents: diff changeset	90 {
93451f832736 Uploaded sblanck parents: diff changeset	91 suppressWarnings(x <- cbind(unlist(map), names(map)))
93451f832736 Uploaded sblanck parents: diff changeset	92 unigene_probe=split(x[,2], x[,1])
93451f832736 Uploaded sblanck parents: diff changeset	93 }
93451f832736 Uploaded sblanck parents: diff changeset	94
93451f832736 Uploaded sblanck parents: diff changeset	95 convert2metaMA<-function(listStudies,mergemeth=mean)
93451f832736 Uploaded sblanck parents: diff changeset	96 {
93451f832736 Uploaded sblanck parents: diff changeset	97 if (!(class(listStudies) %in% c("list"))) {
93451f832736 Uploaded sblanck parents: diff changeset	98 stop("listStudies must be a list")
93451f832736 Uploaded sblanck parents: diff changeset	99 }
93451f832736 Uploaded sblanck parents: diff changeset	100 conv_unigene=lapply(listStudies,
93451f832736 Uploaded sblanck parents: diff changeset	101 FUN=function(x) unigene2probe(probe2unigene(x)))
93451f832736 Uploaded sblanck parents: diff changeset	102
93451f832736 Uploaded sblanck parents: diff changeset	103 id=lapply(conv_unigene,names)
93451f832736 Uploaded sblanck parents: diff changeset	104 inter=Reduce(intersect,id)
93451f832736 Uploaded sblanck parents: diff changeset	105 if(length(inter)<=0){stop("no common genes")}
93451f832736 Uploaded sblanck parents: diff changeset	106 print(paste(length(inter),"genes in common"))
93451f832736 Uploaded sblanck parents: diff changeset	107 esets=lapply(1:length(listStudies),FUN=function(i){
93451f832736 Uploaded sblanck parents: diff changeset	108 l=lapply(conv_unigene[[i]][inter],
93451f832736 Uploaded sblanck parents: diff changeset	109 FUN=function(x) exprs(listStudies[[i]])[x,,drop=TRUE])
93451f832736 Uploaded sblanck parents: diff changeset	110 esetsgr=t(sapply(l,FUN=function(ll) if(is.null(dim(ll))){ll}
93451f832736 Uploaded sblanck parents: diff changeset	111 else{apply(ll,2,mergemeth)}))
93451f832736 Uploaded sblanck parents: diff changeset	112 esetsgr
93451f832736 Uploaded sblanck parents: diff changeset	113 })
93451f832736 Uploaded sblanck parents: diff changeset	114 return(list(esets=esets,conv.unigene=conv_unigene))
93451f832736 Uploaded sblanck parents: diff changeset	115 }
93451f832736 Uploaded sblanck parents: diff changeset	116
93451f832736 Uploaded sblanck parents: diff changeset	117 normalization<-function(data){
93451f832736 Uploaded sblanck parents: diff changeset	118 ex <- exprs(data)
93451f832736 Uploaded sblanck parents: diff changeset	119 qx <- as.numeric(quantile(ex, c(0., 0.25, 0.5, 0.75, 0.99, 1.0), na.rm=T))
93451f832736 Uploaded sblanck parents: diff changeset	120 LogC <- (qx[5] > 100) \|\|
93451f832736 Uploaded sblanck parents: diff changeset	121 (qx[6]-qx[1] > 50 && qx[2] > 0) \|\|
93451f832736 Uploaded sblanck parents: diff changeset	122 (qx[2] > 0 && qx[2] < 1 && qx[4] > 1 && qx[4] < 2)
93451f832736 Uploaded sblanck parents: diff changeset	123 if (LogC) { ex[which(ex <= 0)] <- NaN
93451f832736 Uploaded sblanck parents: diff changeset	124 return (log2(ex)) } else {
93451f832736 Uploaded sblanck parents: diff changeset	125 return (ex)
93451f832736 Uploaded sblanck parents: diff changeset	126 }
93451f832736 Uploaded sblanck parents: diff changeset	127 }
93451f832736 Uploaded sblanck parents: diff changeset	128
93451f832736 Uploaded sblanck parents: diff changeset	129
93451f832736 Uploaded sblanck parents: diff changeset	130 filterCondition<-function(gset,condition1, condition2){
93451f832736 Uploaded sblanck parents: diff changeset	131 selected=c(which((tolower(as.character(pData(gset)["source_name_ch1"][,1]))==condition1)),
93451f832736 Uploaded sblanck parents: diff changeset	132 which(tolower(as.character(pData(gset)["source_name_ch1"][,1]))==condition2))
93451f832736 Uploaded sblanck parents: diff changeset	133
93451f832736 Uploaded sblanck parents: diff changeset	134 return(gset[,selected])
93451f832736 Uploaded sblanck parents: diff changeset	135 }
93451f832736 Uploaded sblanck parents: diff changeset	136
93451f832736 Uploaded sblanck parents: diff changeset	137 rdatalist <- lapply(rdataList, FUN=function(datalist) normalization(datalist))
93451f832736 Uploaded sblanck parents: diff changeset	138
93451f832736 Uploaded sblanck parents: diff changeset	139 classes=list()
93451f832736 Uploaded sblanck parents: diff changeset	140 filteredRdataList=list()
93451f832736 Uploaded sblanck parents: diff changeset	141 for (i in 1:length(rdatalist))
93451f832736 Uploaded sblanck parents: diff changeset	142 {
93451f832736 Uploaded sblanck parents: diff changeset	143 currentData=rdataList[[i]]
93451f832736 Uploaded sblanck parents: diff changeset	144 currentCondition1=condition1List[[i]]
93451f832736 Uploaded sblanck parents: diff changeset	145 currentCondition2=condition2List[[i]]
93451f832736 Uploaded sblanck parents: diff changeset	146 #currentData=filterCondition(currentData,currentCondition1,currentCondition2)
93451f832736 Uploaded sblanck parents: diff changeset	147 currentClasses=as.numeric(tolower(as.character(pData(currentData)["source_name_ch1"][,1]))==currentCondition1)
93451f832736 Uploaded sblanck parents: diff changeset	148 filteredRdataList=c(filteredRdataList,currentData)
93451f832736 Uploaded sblanck parents: diff changeset	149 classes=c(classes,list(currentClasses))
93451f832736 Uploaded sblanck parents: diff changeset	150 #write(file="~/galaxy-modal/classes.txt",classes)
93451f832736 Uploaded sblanck parents: diff changeset	151 }
93451f832736 Uploaded sblanck parents: diff changeset	152
93451f832736 Uploaded sblanck parents: diff changeset	153 #rdataList=filteredRdataList
93451f832736 Uploaded sblanck parents: diff changeset	154 conv=convert2metaMA(rdataList)
93451f832736 Uploaded sblanck parents: diff changeset	155 esets=conv$esets
93451f832736 Uploaded sblanck parents: diff changeset	156 conv_unigene=conv$conv.unigene
93451f832736 Uploaded sblanck parents: diff changeset	157
93451f832736 Uploaded sblanck parents: diff changeset	158 #write(file="~/galaxy-modal/esets.txt",length(esets))
93451f832736 Uploaded sblanck parents: diff changeset	159 #write(file="~/galaxy-modal/classes.txt",length(classes))
93451f832736 Uploaded sblanck parents: diff changeset	160 res=pvalcombination(esets=esets,classes=classes,moderated="limma")
93451f832736 Uploaded sblanck parents: diff changeset	161 resIDDIRR=IDDIRR(res$Meta,res$AllIndStudies)
93451f832736 Uploaded sblanck parents: diff changeset	162 length(res$Meta)
93451f832736 Uploaded sblanck parents: diff changeset	163 Hs.Meta=rownames(esets[[1]])[res$Meta]
93451f832736 Uploaded sblanck parents: diff changeset	164 origId.Meta=lapply(conv_unigene,FUN=function(vec) as.vector(unlist(vec[Hs.Meta])))
93451f832736 Uploaded sblanck parents: diff changeset	165
93451f832736 Uploaded sblanck parents: diff changeset	166 gpllist <- lapply(rdataList, FUN=function(ann) annotation(ann))
93451f832736 Uploaded sblanck parents: diff changeset	167 platflist <- lapply(gpllist, FUN=function(gpl) getGEO(gpl, AnnotGPL=TRUE))
93451f832736 Uploaded sblanck parents: diff changeset	168 ncbifdlist <- lapply(platflist, FUN=function(data) data.frame(attr(dataTable(data), "table")))
93451f832736 Uploaded sblanck parents: diff changeset	169 ncbifdresult=lapply(1:length(origId.Meta), FUN=function(i) ncbifdlist[[i]][which(ncbifdlist[[i]]$ID %in% origId.Meta[[i]]),])
93451f832736 Uploaded sblanck parents: diff changeset	170 ncbidfannot=do.call(rbind,ncbifdresult)
93451f832736 Uploaded sblanck parents: diff changeset	171 ncbidfannot <- subset(ncbidfannot, select=c("Platform_SPOTID","ID","Gene.symbol","Gene.title","Gene.ID","Chromosome.annotation","GO.Function.ID"))
93451f832736 Uploaded sblanck parents: diff changeset	172
93451f832736 Uploaded sblanck parents: diff changeset	173 library(jsonlite)
93451f832736 Uploaded sblanck parents: diff changeset	174 matrixncbidfannot=as.matrix(ncbidfannot)
93451f832736 Uploaded sblanck parents: diff changeset	175 datajson=toJSON(matrixncbidfannot,pretty = TRUE)
93451f832736 Uploaded sblanck parents: diff changeset	176 summaryjson=toJSON(as.matrix(t(resIDDIRR)),pretty = TRUE)
93451f832736 Uploaded sblanck parents: diff changeset	177
93451f832736 Uploaded sblanck parents: diff changeset	178
93451f832736 Uploaded sblanck parents: diff changeset	179 #vennsplit=strsplit(result.venn,split="/")[[1]]
93451f832736 Uploaded sblanck parents: diff changeset	180 #venn=paste0("./",vennsplit[length(vennsplit)])
93451f832736 Uploaded sblanck parents: diff changeset	181
93451f832736 Uploaded sblanck parents: diff changeset	182
93451f832736 Uploaded sblanck parents: diff changeset	183 vennFilename="venn.png"
93451f832736 Uploaded sblanck parents: diff changeset	184 vennFile=file.path(result.path,vennFilename)
93451f832736 Uploaded sblanck parents: diff changeset	185 htmlfile=readChar(result.template, file.info(result.template)$size)
93451f832736 Uploaded sblanck parents: diff changeset	186 htmlfile=gsub(x=htmlfile,pattern = "###DATAJSON###",replacement = datajson, fixed = TRUE)
93451f832736 Uploaded sblanck parents: diff changeset	187 htmlfile=gsub(x=htmlfile,pattern = "###SUMMARYJSON###",replacement = summaryjson, fixed = TRUE)
93451f832736 Uploaded sblanck parents: diff changeset	188 htmlfile=gsub(x=htmlfile,pattern = "###VENN###",replacement = vennFilename, fixed = TRUE)
93451f832736 Uploaded sblanck parents: diff changeset	189 write(htmlfile,result.html)
93451f832736 Uploaded sblanck parents: diff changeset	190
93451f832736 Uploaded sblanck parents: diff changeset	191 library(VennDiagram)
93451f832736 Uploaded sblanck parents: diff changeset	192 flog.threshold(ERROR)
93451f832736 Uploaded sblanck parents: diff changeset	193
93451f832736 Uploaded sblanck parents: diff changeset	194 #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")
93451f832736 Uploaded sblanck parents: diff changeset	195 dir.create(result.path, showWarnings = TRUE, recursive = FALSE)
93451f832736 Uploaded sblanck parents: diff changeset	196
93451f832736 Uploaded sblanck parents: diff changeset	197 showVenn<-function(liste,file)
93451f832736 Uploaded sblanck parents: diff changeset	198 {
93451f832736 Uploaded sblanck parents: diff changeset	199 venn.plot<-venn.diagram(x = liste,
93451f832736 Uploaded sblanck parents: diff changeset	200 filename = vennFilename, col = "black",
93451f832736 Uploaded sblanck parents: diff changeset	201 fill = 1:length(liste)+1,
93451f832736 Uploaded sblanck parents: diff changeset	202 margin=0.05, alpha = 0.6,imagetype = "png")
93451f832736 Uploaded sblanck parents: diff changeset	203 # png(file);
93451f832736 Uploaded sblanck parents: diff changeset	204 # grid.draw(venn.plot);
93451f832736 Uploaded sblanck parents: diff changeset	205 # dev.off();
93451f832736 Uploaded sblanck parents: diff changeset	206
93451f832736 Uploaded sblanck parents: diff changeset	207 }
93451f832736 Uploaded sblanck parents: diff changeset	208
93451f832736 Uploaded sblanck parents: diff changeset	209 l=list()
93451f832736 Uploaded sblanck parents: diff changeset	210 for(i in 1:length(esets))
93451f832736 Uploaded sblanck parents: diff changeset	211 {
93451f832736 Uploaded sblanck parents: diff changeset	212 l[[paste("study",i,sep="")]]<-res[[i]]
93451f832736 Uploaded sblanck parents: diff changeset	213 }
93451f832736 Uploaded sblanck parents: diff changeset	214 l[["Meta"]]=res[[length(res)-1]]
93451f832736 Uploaded sblanck parents: diff changeset	215 showVenn(l,vennFile)
93451f832736 Uploaded sblanck parents: diff changeset	216 file.copy(vennFilename,result.path)
93451f832736 Uploaded sblanck parents: diff changeset	217 #l=list()
93451f832736 Uploaded sblanck parents: diff changeset	218 #for(i in 1:length(esets))
93451f832736 Uploaded sblanck parents: diff changeset	219 #{
93451f832736 Uploaded sblanck parents: diff changeset	220 # l[[paste("study",i,sep="")]]<-res[[i]]
93451f832736 Uploaded sblanck parents: diff changeset	221 #}
93451f832736 Uploaded sblanck parents: diff changeset	222 #l[["Meta"]]=res[[length(res)-1]]
93451f832736 Uploaded sblanck parents: diff changeset	223 #showVenn(res,result.venn)
93451f832736 Uploaded sblanck parents: diff changeset	224 #writeLines(c("<h2>Venn diagram</h2>"),file.conn)
93451f832736 Uploaded sblanck parents: diff changeset	225 #writeLines(c("<img src='venn.png'><br/><br/>"),file.conn)
93451f832736 Uploaded sblanck parents: diff changeset	226 #writeLines(c("</body></html>"),file.conn)
93451f832736 Uploaded sblanck parents: diff changeset	227 #close(file.conn)

Mercurial > repos > sblanck > smagexp

annotate MetaMA.R @ 21:f953fdee364c draft