smagexp: MetaMA.R annotate

annotate MetaMA.R @ 36:22e1325aaa88 draft

planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 0d3497e4f84869670647f7a6ffceca64469a4c00

author	sblanck
date	Fri, 22 Jun 2018 04:30:31 -0400
parents	f953fdee364c
children

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))
36 22e1325aaa88 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 0d3497e4f84869670647f7a6ffceca64469a4c00 sblanck parents: 21 diff changeset	38 suppressPackageStartupMessages(require(UpSetR))
9 328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 2 diff changeset	39
328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 2 diff changeset	40 listInput <- trimws( unlist( strsplit(trimws(opt$input), ",") ) )
20 a4015af2ae12 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit a25677963b28019d4434bbe411b28168c912d71d sblanck parents: 10 diff changeset	41 species=opt$species
9 328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 2 diff changeset	42
2 93451f832736 Uploaded sblanck parents: diff changeset	43 rdataList=list()
93451f832736 Uploaded sblanck parents: diff changeset	44 condition1List=list()
93451f832736 Uploaded sblanck parents: diff changeset	45 condition2List=list()
9 328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 2 diff changeset	46 for (input in listInput)
2 93451f832736 Uploaded sblanck parents: diff changeset	47 {
9 328f4031e5d3 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty sblanck parents: 2 diff changeset	48 load(input)
2 93451f832736 Uploaded sblanck parents: diff changeset	49
93451f832736 Uploaded sblanck parents: diff changeset	50 rdataList=c(rdataList,(eset))
93451f832736 Uploaded sblanck parents: diff changeset	51 condition1List=c(condition1List,saveConditions[1])
93451f832736 Uploaded sblanck parents: diff changeset	52 condition2List=c(condition2List,saveConditions[2])
93451f832736 Uploaded sblanck parents: diff changeset	53
93451f832736 Uploaded sblanck parents: diff changeset	54 }
93451f832736 Uploaded sblanck parents: diff changeset	55
10 56267e3293b2 planemo upload commit 0ad899de37d891f387912b7abd63506605a25976-dirty sblanck parents: 9 diff changeset	56 result.html<-opt$htmloutput
56267e3293b2 planemo upload commit 0ad899de37d891f387912b7abd63506605a25976-dirty sblanck parents: 9 diff changeset	57 result.path<-opt$htmloutputpath
56267e3293b2 planemo upload commit 0ad899de37d891f387912b7abd63506605a25976-dirty sblanck parents: 9 diff changeset	58 result.template<-opt$htmltemplate
2 93451f832736 Uploaded sblanck parents: diff changeset	59
36 22e1325aaa88 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 0d3497e4f84869670647f7a6ffceca64469a4c00 sblanck parents: 21 diff changeset	60 #showVenn<-function(res,file)
22e1325aaa88 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 0d3497e4f84869670647f7a6ffceca64469a4c00 sblanck parents: 21 diff changeset	61 #{
22e1325aaa88 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 0d3497e4f84869670647f7a6ffceca64469a4c00 sblanck parents: 21 diff changeset	62 # venn.plot<-venn.diagram(x = c(res[c(1:(length(res)-3))],meta=list(res$Meta)),
22e1325aaa88 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 0d3497e4f84869670647f7a6ffceca64469a4c00 sblanck parents: 21 diff changeset	63 # filename = NULL, col = "black",
22e1325aaa88 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 0d3497e4f84869670647f7a6ffceca64469a4c00 sblanck parents: 21 diff changeset	64 # fill = c(1:(length(res)-2)),
22e1325aaa88 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 0d3497e4f84869670647f7a6ffceca64469a4c00 sblanck parents: 21 diff changeset	65 # margin=0.05, alpha = 0.6)
22e1325aaa88 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 0d3497e4f84869670647f7a6ffceca64469a4c00 sblanck parents: 21 diff changeset	66 # jpeg(file)
22e1325aaa88 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 0d3497e4f84869670647f7a6ffceca64469a4c00 sblanck parents: 21 diff changeset	67 # grid.draw(venn.plot)
22e1325aaa88 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 0d3497e4f84869670647f7a6ffceca64469a4c00 sblanck parents: 21 diff changeset	68 # dev.off()
22e1325aaa88 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 0d3497e4f84869670647f7a6ffceca64469a4c00 sblanck parents: 21 diff changeset	69 #}
2 93451f832736 Uploaded sblanck parents: diff changeset	70
20 a4015af2ae12 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit a25677963b28019d4434bbe411b28168c912d71d sblanck parents: 10 diff changeset	71 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	72 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	73 biocLite(species)
a4015af2ae12 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit a25677963b28019d4434bbe411b28168c912d71d sblanck parents: 10 diff changeset	74 }
a4015af2ae12 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit a25677963b28019d4434bbe411b28168c912d71d sblanck parents: 10 diff changeset	75
36 22e1325aaa88 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 0d3497e4f84869670647f7a6ffceca64469a4c00 sblanck parents: 21 diff changeset	76 library(species,character.only = TRUE)
2 93451f832736 Uploaded sblanck parents: diff changeset	77 x <- org.Hs.egUNIGENE
93451f832736 Uploaded sblanck parents: diff changeset	78 mapped_genes <- mappedkeys(x)
93451f832736 Uploaded sblanck parents: diff changeset	79 link <- as.list(x[mapped_genes])
93451f832736 Uploaded sblanck parents: diff changeset	80
93451f832736 Uploaded sblanck parents: diff changeset	81 probe2unigene<-function(expset){
93451f832736 Uploaded sblanck parents: diff changeset	82 #construction of the map probe->unigene
93451f832736 Uploaded sblanck parents: diff changeset	83 probes=rownames(exprs(expset))
93451f832736 Uploaded sblanck parents: diff changeset	84 gene_id=fData(expset)[probes,"ENTREZ_GENE_ID"]
93451f832736 Uploaded sblanck parents: diff changeset	85 unigene=link[gene_id]
93451f832736 Uploaded sblanck parents: diff changeset	86 names(unigene)<-probes
93451f832736 Uploaded sblanck parents: diff changeset	87 probe_unigene=unigene
93451f832736 Uploaded sblanck parents: diff changeset	88 }
93451f832736 Uploaded sblanck parents: diff changeset	89
93451f832736 Uploaded sblanck parents: diff changeset	90 unigene2probe<-function(map)
93451f832736 Uploaded sblanck parents: diff changeset	91 {
93451f832736 Uploaded sblanck parents: diff changeset	92 suppressWarnings(x <- cbind(unlist(map), names(map)))
93451f832736 Uploaded sblanck parents: diff changeset	93 unigene_probe=split(x[,2], x[,1])
93451f832736 Uploaded sblanck parents: diff changeset	94 }
93451f832736 Uploaded sblanck parents: diff changeset	95
93451f832736 Uploaded sblanck parents: diff changeset	96 convert2metaMA<-function(listStudies,mergemeth=mean)
93451f832736 Uploaded sblanck parents: diff changeset	97 {
93451f832736 Uploaded sblanck parents: diff changeset	98 if (!(class(listStudies) %in% c("list"))) {
93451f832736 Uploaded sblanck parents: diff changeset	99 stop("listStudies must be a list")
93451f832736 Uploaded sblanck parents: diff changeset	100 }
93451f832736 Uploaded sblanck parents: diff changeset	101 conv_unigene=lapply(listStudies,
93451f832736 Uploaded sblanck parents: diff changeset	102 FUN=function(x) unigene2probe(probe2unigene(x)))
93451f832736 Uploaded sblanck parents: diff changeset	103
93451f832736 Uploaded sblanck parents: diff changeset	104 id=lapply(conv_unigene,names)
93451f832736 Uploaded sblanck parents: diff changeset	105 inter=Reduce(intersect,id)
93451f832736 Uploaded sblanck parents: diff changeset	106 if(length(inter)<=0){stop("no common genes")}
93451f832736 Uploaded sblanck parents: diff changeset	107 print(paste(length(inter),"genes in common"))
93451f832736 Uploaded sblanck parents: diff changeset	108 esets=lapply(1:length(listStudies),FUN=function(i){
93451f832736 Uploaded sblanck parents: diff changeset	109 l=lapply(conv_unigene[[i]][inter],
93451f832736 Uploaded sblanck parents: diff changeset	110 FUN=function(x) exprs(listStudies[[i]])[x,,drop=TRUE])
93451f832736 Uploaded sblanck parents: diff changeset	111 esetsgr=t(sapply(l,FUN=function(ll) if(is.null(dim(ll))){ll}
93451f832736 Uploaded sblanck parents: diff changeset	112 else{apply(ll,2,mergemeth)}))
93451f832736 Uploaded sblanck parents: diff changeset	113 esetsgr
93451f832736 Uploaded sblanck parents: diff changeset	114 })
93451f832736 Uploaded sblanck parents: diff changeset	115 return(list(esets=esets,conv.unigene=conv_unigene))
93451f832736 Uploaded sblanck parents: diff changeset	116 }
93451f832736 Uploaded sblanck parents: diff changeset	117
93451f832736 Uploaded sblanck parents: diff changeset	118 normalization<-function(data){
93451f832736 Uploaded sblanck parents: diff changeset	119 ex <- exprs(data)
93451f832736 Uploaded sblanck parents: diff changeset	120 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	121 LogC <- (qx[5] > 100) \|\|
93451f832736 Uploaded sblanck parents: diff changeset	122 (qx[6]-qx[1] > 50 && qx[2] > 0) \|\|
93451f832736 Uploaded sblanck parents: diff changeset	123 (qx[2] > 0 && qx[2] < 1 && qx[4] > 1 && qx[4] < 2)
93451f832736 Uploaded sblanck parents: diff changeset	124 if (LogC) { ex[which(ex <= 0)] <- NaN
93451f832736 Uploaded sblanck parents: diff changeset	125 return (log2(ex)) } else {
93451f832736 Uploaded sblanck parents: diff changeset	126 return (ex)
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
93451f832736 Uploaded sblanck parents: diff changeset	131 filterCondition<-function(gset,condition1, condition2){
93451f832736 Uploaded sblanck parents: diff changeset	132 selected=c(which((tolower(as.character(pData(gset)["source_name_ch1"][,1]))==condition1)),
93451f832736 Uploaded sblanck parents: diff changeset	133 which(tolower(as.character(pData(gset)["source_name_ch1"][,1]))==condition2))
93451f832736 Uploaded sblanck parents: diff changeset	134
93451f832736 Uploaded sblanck parents: diff changeset	135 return(gset[,selected])
93451f832736 Uploaded sblanck parents: diff changeset	136 }
93451f832736 Uploaded sblanck parents: diff changeset	137
93451f832736 Uploaded sblanck parents: diff changeset	138 rdatalist <- lapply(rdataList, FUN=function(datalist) normalization(datalist))
93451f832736 Uploaded sblanck parents: diff changeset	139
93451f832736 Uploaded sblanck parents: diff changeset	140 classes=list()
93451f832736 Uploaded sblanck parents: diff changeset	141 filteredRdataList=list()
93451f832736 Uploaded sblanck parents: diff changeset	142 for (i in 1:length(rdatalist))
93451f832736 Uploaded sblanck parents: diff changeset	143 {
93451f832736 Uploaded sblanck parents: diff changeset	144 currentData=rdataList[[i]]
93451f832736 Uploaded sblanck parents: diff changeset	145 currentCondition1=condition1List[[i]]
93451f832736 Uploaded sblanck parents: diff changeset	146 currentCondition2=condition2List[[i]]
93451f832736 Uploaded sblanck parents: diff changeset	147 #currentData=filterCondition(currentData,currentCondition1,currentCondition2)
93451f832736 Uploaded sblanck parents: diff changeset	148 currentClasses=as.numeric(tolower(as.character(pData(currentData)["source_name_ch1"][,1]))==currentCondition1)
93451f832736 Uploaded sblanck parents: diff changeset	149 filteredRdataList=c(filteredRdataList,currentData)
93451f832736 Uploaded sblanck parents: diff changeset	150 classes=c(classes,list(currentClasses))
93451f832736 Uploaded sblanck parents: diff changeset	151 #write(file="~/galaxy-modal/classes.txt",classes)
93451f832736 Uploaded sblanck parents: diff changeset	152 }
93451f832736 Uploaded sblanck parents: diff changeset	153
93451f832736 Uploaded sblanck parents: diff changeset	154 #rdataList=filteredRdataList
93451f832736 Uploaded sblanck parents: diff changeset	155 conv=convert2metaMA(rdataList)
93451f832736 Uploaded sblanck parents: diff changeset	156 esets=conv$esets
93451f832736 Uploaded sblanck parents: diff changeset	157 conv_unigene=conv$conv.unigene
93451f832736 Uploaded sblanck parents: diff changeset	158
93451f832736 Uploaded sblanck parents: diff changeset	159 #write(file="~/galaxy-modal/esets.txt",length(esets))
93451f832736 Uploaded sblanck parents: diff changeset	160 #write(file="~/galaxy-modal/classes.txt",length(classes))
93451f832736 Uploaded sblanck parents: diff changeset	161 res=pvalcombination(esets=esets,classes=classes,moderated="limma")
93451f832736 Uploaded sblanck parents: diff changeset	162 resIDDIRR=IDDIRR(res$Meta,res$AllIndStudies)
36 22e1325aaa88 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 0d3497e4f84869670647f7a6ffceca64469a4c00 sblanck parents: 21 diff changeset	163 #length(res$Meta)
2 93451f832736 Uploaded sblanck parents: diff changeset	164 Hs.Meta=rownames(esets[[1]])[res$Meta]
93451f832736 Uploaded sblanck parents: diff changeset	165 origId.Meta=lapply(conv_unigene,FUN=function(vec) as.vector(unlist(vec[Hs.Meta])))
93451f832736 Uploaded sblanck parents: diff changeset	166
93451f832736 Uploaded sblanck parents: diff changeset	167 gpllist <- lapply(rdataList, FUN=function(ann) annotation(ann))
93451f832736 Uploaded sblanck parents: diff changeset	168 platflist <- lapply(gpllist, FUN=function(gpl) getGEO(gpl, AnnotGPL=TRUE))
93451f832736 Uploaded sblanck parents: diff changeset	169 ncbifdlist <- lapply(platflist, FUN=function(data) data.frame(attr(dataTable(data), "table")))
93451f832736 Uploaded sblanck parents: diff changeset	170 ncbifdresult=lapply(1:length(origId.Meta), FUN=function(i) ncbifdlist[[i]][which(ncbifdlist[[i]]$ID %in% origId.Meta[[i]]),])
93451f832736 Uploaded sblanck parents: diff changeset	171 ncbidfannot=do.call(rbind,ncbifdresult)
93451f832736 Uploaded sblanck parents: diff changeset	172 ncbidfannot <- subset(ncbidfannot, select=c("Platform_SPOTID","ID","Gene.symbol","Gene.title","Gene.ID","Chromosome.annotation","GO.Function.ID"))
93451f832736 Uploaded sblanck parents: diff changeset	173
93451f832736 Uploaded sblanck parents: diff changeset	174 library(jsonlite)
93451f832736 Uploaded sblanck parents: diff changeset	175 matrixncbidfannot=as.matrix(ncbidfannot)
93451f832736 Uploaded sblanck parents: diff changeset	176 datajson=toJSON(matrixncbidfannot,pretty = TRUE)
93451f832736 Uploaded sblanck parents: diff changeset	177 summaryjson=toJSON(as.matrix(t(resIDDIRR)),pretty = TRUE)
93451f832736 Uploaded sblanck parents: diff changeset	178
93451f832736 Uploaded sblanck parents: diff changeset	179
93451f832736 Uploaded sblanck parents: diff changeset	180 #vennsplit=strsplit(result.venn,split="/")[[1]]
93451f832736 Uploaded sblanck parents: diff changeset	181 #venn=paste0("./",vennsplit[length(vennsplit)])
93451f832736 Uploaded sblanck parents: diff changeset	182
93451f832736 Uploaded sblanck parents: diff changeset	183
93451f832736 Uploaded sblanck parents: diff changeset	184 vennFilename="venn.png"
93451f832736 Uploaded sblanck parents: diff changeset	185 vennFile=file.path(result.path,vennFilename)
93451f832736 Uploaded sblanck parents: diff changeset	186 library(VennDiagram)
93451f832736 Uploaded sblanck parents: diff changeset	187 flog.threshold(ERROR)
93451f832736 Uploaded sblanck parents: diff changeset	188
93451f832736 Uploaded sblanck parents: diff changeset	189 #venn.plot<-venn.diagram(x = c(res[c(1:(length(res)-3))],meta=list(res$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	190 dir.create(result.path, showWarnings = TRUE, recursive = FALSE)
93451f832736 Uploaded sblanck parents: diff changeset	191
93451f832736 Uploaded sblanck parents: diff changeset	192 showVenn<-function(liste,file)
93451f832736 Uploaded sblanck parents: diff changeset	193 {
93451f832736 Uploaded sblanck parents: diff changeset	194 venn.plot<-venn.diagram(x = liste,
93451f832736 Uploaded sblanck parents: diff changeset	195 filename = vennFilename, col = "black",
93451f832736 Uploaded sblanck parents: diff changeset	196 fill = 1:length(liste)+1,
93451f832736 Uploaded sblanck parents: diff changeset	197 margin=0.05, alpha = 0.6,imagetype = "png")
93451f832736 Uploaded sblanck parents: diff changeset	198 # png(file);
93451f832736 Uploaded sblanck parents: diff changeset	199 # grid.draw(venn.plot);
93451f832736 Uploaded sblanck parents: diff changeset	200 # dev.off();
93451f832736 Uploaded sblanck parents: diff changeset	201
93451f832736 Uploaded sblanck parents: diff changeset	202 }
93451f832736 Uploaded sblanck parents: diff changeset	203
93451f832736 Uploaded sblanck parents: diff changeset	204 l=list()
93451f832736 Uploaded sblanck parents: diff changeset	205 for(i in 1:length(esets))
93451f832736 Uploaded sblanck parents: diff changeset	206 {
93451f832736 Uploaded sblanck parents: diff changeset	207 l[[paste("study",i,sep="")]]<-res[[i]]
93451f832736 Uploaded sblanck parents: diff changeset	208 }
93451f832736 Uploaded sblanck parents: diff changeset	209 l[["Meta"]]=res[[length(res)-1]]
36 22e1325aaa88 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 0d3497e4f84869670647f7a6ffceca64469a4c00 sblanck parents: 21 diff changeset	210
22e1325aaa88 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 0d3497e4f84869670647f7a6ffceca64469a4c00 sblanck parents: 21 diff changeset	211 if (length(l)<5) {
22e1325aaa88 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 0d3497e4f84869670647f7a6ffceca64469a4c00 sblanck parents: 21 diff changeset	212 title="Venn diagram"
22e1325aaa88 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 0d3497e4f84869670647f7a6ffceca64469a4c00 sblanck parents: 21 diff changeset	213 width=500
22e1325aaa88 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 0d3497e4f84869670647f7a6ffceca64469a4c00 sblanck parents: 21 diff changeset	214 showVenn(l,vennFile)
22e1325aaa88 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 0d3497e4f84869670647f7a6ffceca64469a4c00 sblanck parents: 21 diff changeset	215 } else {
22e1325aaa88 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 0d3497e4f84869670647f7a6ffceca64469a4c00 sblanck parents: 21 diff changeset	216 title="Upsetr diagram"
22e1325aaa88 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 0d3497e4f84869670647f7a6ffceca64469a4c00 sblanck parents: 21 diff changeset	217 width=1000
22e1325aaa88 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 0d3497e4f84869670647f7a6ffceca64469a4c00 sblanck parents: 21 diff changeset	218 png(vennFile,width=width,height=500)
22e1325aaa88 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 0d3497e4f84869670647f7a6ffceca64469a4c00 sblanck parents: 21 diff changeset	219 upset(fromList(as.list(l)), order.by = "freq")
22e1325aaa88 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 0d3497e4f84869670647f7a6ffceca64469a4c00 sblanck parents: 21 diff changeset	220 dev.off()
22e1325aaa88 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 0d3497e4f84869670647f7a6ffceca64469a4c00 sblanck parents: 21 diff changeset	221 }
22e1325aaa88 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 0d3497e4f84869670647f7a6ffceca64469a4c00 sblanck parents: 21 diff changeset	222
2 93451f832736 Uploaded sblanck parents: diff changeset	223 file.copy(vennFilename,result.path)
36 22e1325aaa88 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 0d3497e4f84869670647f7a6ffceca64469a4c00 sblanck parents: 21 diff changeset	224
22e1325aaa88 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 0d3497e4f84869670647f7a6ffceca64469a4c00 sblanck parents: 21 diff changeset	225 htmlfile=readChar(result.template, file.info(result.template)$size)
22e1325aaa88 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 0d3497e4f84869670647f7a6ffceca64469a4c00 sblanck parents: 21 diff changeset	226 htmlfile=gsub(x=htmlfile,pattern = "###DATAJSON###",replacement = datajson, fixed = TRUE)
22e1325aaa88 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 0d3497e4f84869670647f7a6ffceca64469a4c00 sblanck parents: 21 diff changeset	227 htmlfile=gsub(x=htmlfile,pattern = "###SUMMARYJSON###",replacement = summaryjson, fixed = TRUE)
22e1325aaa88 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 0d3497e4f84869670647f7a6ffceca64469a4c00 sblanck parents: 21 diff changeset	228 htmlfile=gsub(x=htmlfile,pattern = "###VENN###",replacement = vennFilename, fixed = TRUE)
22e1325aaa88 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 0d3497e4f84869670647f7a6ffceca64469a4c00 sblanck parents: 21 diff changeset	229 tmlfile=gsub(x=htmlfile,pattern = "###WIDTH###",replacement = as.character(width), fixed = TRUE)
22e1325aaa88 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 0d3497e4f84869670647f7a6ffceca64469a4c00 sblanck parents: 21 diff changeset	230 htmlfile=gsub(x=htmlfile,pattern = "###TITLE###",replacement = title, fixed = TRUE)
22e1325aaa88 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 0d3497e4f84869670647f7a6ffceca64469a4c00 sblanck parents: 21 diff changeset	231 write(htmlfile,result.html)
2 93451f832736 Uploaded sblanck parents: diff changeset	232 #l=list()
93451f832736 Uploaded sblanck parents: diff changeset	233 #for(i in 1:length(esets))
93451f832736 Uploaded sblanck parents: diff changeset	234 #{
93451f832736 Uploaded sblanck parents: diff changeset	235 # l[[paste("study",i,sep="")]]<-res[[i]]
93451f832736 Uploaded sblanck parents: diff changeset	236 #}
93451f832736 Uploaded sblanck parents: diff changeset	237 #l[["Meta"]]=res[[length(res)-1]]
93451f832736 Uploaded sblanck parents: diff changeset	238 #showVenn(res,result.venn)
93451f832736 Uploaded sblanck parents: diff changeset	239 #writeLines(c("<h2>Venn diagram</h2>"),file.conn)
93451f832736 Uploaded sblanck parents: diff changeset	240 #writeLines(c("<img src='venn.png'><br/><br/>"),file.conn)
93451f832736 Uploaded sblanck parents: diff changeset	241 #writeLines(c("</body></html>"),file.conn)
36 22e1325aaa88 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 0d3497e4f84869670647f7a6ffceca64469a4c00 sblanck parents: 21 diff changeset	242 #close(file.conn)

Mercurial > repos > sblanck > smagexp

annotate MetaMA.R @ 36:22e1325aaa88 draft