annotate Analyse.R @ 8:e4e6e583b8d9 draft default tip

planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit ad301f84e16455ca3886e9b56e908180dfd66d4f

#!/usr/bin/env Rscript
# setup R error handling to go to stderr
options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )

# we need that to not crash galaxy with an UTF8 error on German LC settings.
loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")

library("optparse")

##### Read options
option_list=list(
		make_option("--rdatainput",type="character",default="NULL",help="rdata object containing eset object"),
		make_option("--conditions",type="character",default=NULL,help="Text file summarizing conditions of the experiment (required)"),
		make_option("--selectcondition1",type="character",default=NULL,help="log2 transformation"),
#		make_option("--condition1",type="character",default=NULL,help="A table containing the expression data"),
		make_option("--selectcondition2",type="character",default="NULL",help="rdata object containing eset object"),
#		make_option("--condition2",type="character",default=NULL,help="Text file summarizing conditions of the experiment (required)"),
		make_option("--nbresult",type="character",default=NULL,help="number of result displayed results"),
		make_option("--rdataoutput",type="character",default="NULL",help="output rdata object containing eset object"),
		make_option("--htmloutput",type="character",default=NULL,help="Output html report"),
		make_option("--htmloutputpath",type="character",default="NULL",help="Path of output html report"),
		make_option("--tabularoutput",type="character",default=NULL,help="Output text file"),
		make_option("--htmltemplate",type="character",default=NULL,help="html template)"),
		make_option("--tooldirectory",type="character",default=NULL,help="tool directory)")

	
);

opt_parser = OptionParser(option_list=option_list);
opt = parse_args(opt_parser);

if(is.null(opt$rdatainput)){
	print_help(opt_parser)
	stop("rData input required.", call.=FALSE)
}

if(is.null(opt$conditions)){
	print_help(opt_parser)
	stop("conditions input required.", call.=FALSE)
}


#loading libraries
suppressPackageStartupMessages(require(GEOquery))
suppressPackageStartupMessages(require(Biobase))
suppressPackageStartupMessages(require(GEOquery))
suppressPackageStartupMessages(require(GEOmetadb))
suppressPackageStartupMessages(require(limma))
suppressPackageStartupMessages(require(jsonlite))
suppressPackageStartupMessages(require(affy))
suppressPackageStartupMessages(require(dplyr))

load(opt$rdatainput)
targetFile=opt$conditions
condition1Name=opt$selectcondition1
#condition1=opt$condition1
condition2Name=opt$selectcondition2
#condition2=opt$condition2
nbresult=opt$nbresult
result_export_eset=opt$rdataoutput
result=opt$htmloutput
result.path=opt$htmloutputpath
result.tabular=opt$tabularoutput
result.template=opt$htmltemplate
tooldirectory=opt$tooldirectory

targets <- read.table(targetFile,sep="\t",stringsAsFactors=FALSE)

#condition1_tmp <- strsplit(condition1,",")
condition1 <-targets[which(targets$V2==condition1Name),1]

#condition2_tmp <- strsplit(condition2,",")
#condition2<-unlist(condition2_tmp)
condition2 <-targets[which(targets$V2==condition2Name),1]

conditions=c(condition1,condition2)

dir.create(result.path, showWarnings = TRUE, recursive = FALSE)

eset=eset[,which(rownames(eset@phenoData@data) %in% conditions)]

eset@phenoData@data$source_name_ch1=""
eset@phenoData@data$source_name_ch1[which(rownames(eset@phenoData@data) %in% condition1)]=condition1Name
eset@phenoData@data$source_name_ch1[which(rownames(eset@phenoData@data) %in% condition2)]=condition2Name

condNames=paste0("G",as.numeric(as.character(pData(eset)["source_name_ch1"][,1])!=condition1Name))

f <- as.factor(condNames)

design <- model.matrix(~ 0+f)

colnames(design) <- levels(f)

fit <- lmFit(eset, design)

cont.matrix <- makeContrasts(G0-G1, levels=design)

fit2 <- contrasts.fit(fit, cont.matrix)
fit2 <- eBayes(fit2)

tT <- topTable(fit2, adjust="fdr", sort.by="B", number=nbresult)

#head(exprs(eset))

gpl <- annotation(eset)
if (substr(x = gpl,1,3)!="GPL"){
	#if the annotation info does not start with "GPL" we retrieve the corresponding GPL annotation
	mapping=read.csv(paste0(tooldirectory,"/gplToBioc.csv"),stringsAsFactors=FALSE)
	gpl=mapping[which(mapping$bioc_package==annotation(eset)),]$gpl
	gpl=gpl[1]
	
	annotation(eset)=gpl
	
	platf <- getGEO(gpl, AnnotGPL=TRUE)
	ncbifd <- data.frame(attr(dataTable(platf), "table"))
	
	fData(eset)["ID"]=row.names(fData(eset))
	fData(eset)=merge(x=fData(eset),y=ncbifd,all.x = TRUE, by = "ID")
	colnames(fData(eset))[4]="ENTREZ_GENE_ID"
	row.names(fData(eset))=fData(eset)[,"ID"]
	
	tT <- add_rownames(tT, "ID")
	
} else {
	
	gpl <- annotation(eset)
	platf <- getGEO(gpl, AnnotGPL=TRUE)
	ncbifd <- data.frame(attr(dataTable(platf), "table"))
	
	if (!("ID" %in% colnames(tT))){
		tT <- add_rownames(tT, "ID")}
	
}

tT <- merge(tT, ncbifd, by="ID")
tT <- tT[order(tT$P.Value), ] 
tT <- subset(tT, select=c("Platform_SPOTID","ID","adj.P.Val","P.Value","t","B","logFC","Gene.symbol","Gene.title","Gene.ID","Chromosome.annotation","GO.Function.ID"))
tT<-format(tT, digits=2, nsmall=2)
head(tT)
colnames(tT)=gsub(pattern = "\\.",replacement = "_",colnames(tT))
matrixtT=as.matrix(tT)
datajson=toJSON(matrixtT,pretty = TRUE)

htmlfile=readChar(result.template, file.info(result.template)$size)
htmlfile=gsub(x=htmlfile,pattern = "###DATAJSON###",replacement = datajson, fixed = TRUE)
dir.create(result.path, showWarnings = TRUE, recursive = FALSE)

boxplot="boxplot.png"
png(boxplot,width=800,height = 400)
par(mar=c(7,5,1,1))
boxplot(exprs(eset),las=2,outline=FALSE)
dev.off()
htmlfile=gsub(x=htmlfile,pattern = "###BOXPLOT###",replacement = boxplot, fixed = TRUE)
file.copy(boxplot,result.path)

histopvalue="histopvalue.png"

png(histopvalue,width=800,height = 400)
par(mfrow=c(1,2))
hist(fit2$F.p.value,nclass=100,main="Histogram of p-values", xlab="p-values",ylab="frequency")
volcanoplot(fit2,coef=1,highlight=10,main="Volcano plot")
htmlfile=gsub(x=htmlfile,pattern = "###HIST###",replacement = histopvalue, fixed = TRUE)
dev.off()
file.copy(histopvalue,result.path)

saveConditions=c(condition1Name,condition2Name)
save(eset,saveConditions,file=result_export_eset)
write.table(x=tT[,-1],file=result.tabular,quote=FALSE,row.names=FALSE,col.names=TRUE,sep="\t")
write(htmlfile,result)