Mercurial > repos > blankenberglab > gpca
diff r-gpca.R @ 1:d93629e79f5e draft
planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit 3b791d44853d8928046914cd93112bdcf89d4965
| author | blankenberglab |
|---|---|
| date | Tue, 27 Nov 2018 11:02:46 -0500 |
| parents | ed24bacaa4d0 |
| children | 4865e7f4e9c5 |
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--- a/r-gpca.R Mon Nov 19 10:15:19 2018 -0500 +++ b/r-gpca.R Tue Nov 27 11:02:46 2018 -0500 @@ -1,6 +1,7 @@ #!/usr/bin/env Rscript library(optparse) library(gPCA) +options(bitmapType='cairo') # parse options @@ -105,82 +106,92 @@ stop((paste('File for data', opt$data, 'does not exist'))) } -batch<-as.numeric(factor(as.matrix(read.delim(opt$batch, header=TRUE, row.names=1, sep="\t")))) - +dir.create(opt$path); data<-t(as.matrix(read.delim(opt$data, row.names=1, header=TRUE, sep="\t"))) +batch<-as.matrix(read.delim(opt$batch, header=TRUE, row.names=1, sep="\t")) -out<-gPCA.batchdetect(x=data, batch=batch, center=opt$center, scaleY=opt$scaleY, nperm=opt$nperm, filt=opt$filt, seed=opt$seed) +write('<html><body><a name="top"></a>',file = opt$html_outfile, append=TRUE) +write('#Batch\tDelta\tP-value\tCumulative Variance',file = opt$numbers_outfile, append=TRUE) +write('<div align="left><ul id =""><p><b>Table of Contents</b></p></ul></div>', file=opt$html_outfile, append=TRUE) + +for (row in 1:nrow(batch)) { + write(paste0('<li><a href="#',row.names(batch)[row],'">',row.names(batch)[row],'</a></li>'), file=opt$html_outfile, append=TRUE) +} +for (row in 1:nrow(batch)) { + batch1<-as.numeric(factor(batch[row,])) + +out<-gPCA.batchdetect(x=data, batch=batch1, center=opt$center, scaleY=opt$scaleY, nperm=opt$nperm, filt=opt$filt, seed=opt$seed) out$varPCg1<-((out$varPCg1-out$varPCu1)/out$varPCg1)*100 -dir.create(opt$path); - -write.table(data.frame(out$delta, out$p.val, out$varPCg1),file=opt$numbers_outfile, sep="\t", row.name=FALSE, quote=FALSE) +write(paste(row.names(batch)[row],out$delta,out$p.val,out$varPCg1,sep="\t"),file = opt$numbers_outfile, append=TRUE) # General Distribution par(mai=c(0.8,0.8,0.1,0.1),cex=0.8) -png(paste(opt$path,'/gDist.png', sep=""), width=1020, height=800, units='px') +png(paste(opt$path,'/gDist_',row,'.png', sep=""), width=1020, height=800, units='px') gDist(out) invisible(dev.off()) # Guided/Unguided 1v2 par(mai=c(0.8,0.8,0.1,0.1),cex=0.8) -png(paste(opt$path,'/guided_1v2.png', sep=""), width=1020, height=800, units='px') +png(paste(opt$path,'/guided_1v2_',row,'.png', sep=""), width=1020, height=800, units='px') PCplot(out,ug="unguided",type="1v2") invisible(dev.off()) par(mai=c(0.8,0.8,0.1,0.1),cex=0.8) -png(paste(opt$path,'/unguided_1v2.png', sep=""), width=1020, height=800, units='px') +png(paste(opt$path,'/unguided_1v2_',row,'.png', sep=""), width=1020, height=800, units='px') PCplot(out,ug="unguided",type="1v2") invisible(dev.off()) # Guided/Unguided comp,3 par(mai=c(0.65,0.65,0.1,0.1),cex=0.8) -png(paste(opt$path,'/guided_npcs.png', sep=""), width=1020, height=800, units='px') +png(paste(opt$path,'/guided_npcs_',row,'.png', sep=""), width=1020, height=800, units='px') PCplot(out,ug="guided",type="comp",npcs=opt$npcs) invisible(dev.off()) par(mai=c(0.65,0.65,0.1,0.1),cex=0.8) -png(paste(opt$path,'/unguided_npcs.png', sep=""), width=1020, height=800, units='px') +png(paste(opt$path,'/unguided_npcs_',row,'.png', sep=""), width=1020, height=800, units='px') PCplot(out,ug="unguided",type="comp",npcs=opt$npcs) invisible(dev.off()) # Guided/Unguided CumlativeVarPlot par(mai=c(0.8,0.8,0.1,0.1),cex=0.8) -png(paste(opt$path,'/guided_var.png', sep=""), width=1020, height=800, units='px') +png(paste(opt$path,'/guided_var_',row,'.png', sep=""), width=1020, height=800, units='px') CumulativeVarPlot(out,ug="guided",col="blue") invisible(dev.off()) par(mai=c(0.8,0.8,0.1,0.1),cex=0.8) -png(paste(opt$path,'/unguided_var.png', sep=""), width=1020, height=800, units='px') +png(paste(opt$path,'/unguided_var_',row,'.png', sep=""), width=1020, height=800, units='px') CumulativeVarPlot(out,ug="unguided",col="blue") invisible(dev.off()) -write(paste('<html> -<table id="r-gpca-wrap" align="center" border="1"> +write(paste0(' +<header id=',row.names(batch)[row],'><center><font size="11">',row.names(batch)[row],'</font><center></header> +<br> +<table align="center" border="1"> <tr> <th>Delta</th><th>P-value</th><th>varPCg1</th> </tr> <tr> - <td id=delta>',out$delta,'</td><td id=p.val>',out$p.val,'</td><td id=varPCg1>',out$varPCg1,'</td> + <td id="#">',out$delta,'</td><td id=p.val>',out$p.val,'</td><td id=varPCg1>',out$varPCg1,'</td> </tr> </table> +<center><img src="gDist_',row,'.png"/></center><br> +<center><title>Guided 1v2</title><br><img src="guided_1v2_',row,'.png"/></center><br> +<center><title>Unguided 1v2</title><br><img src="unguided_1v2_',row,'.png"/></center><br> -<center><img src="gDist.png"/></center><br> -<center><title>Guided 1v2</title><br><img src="guided_1v2.png"/></center><br> -<center><title>Unguided 1v2</title><br><img src="unguided_1v2.png"/></center><br> +<center><title>Guided Compare to ',opt$npcs,'</title><br><img src="guided_npcs_',row,'.png"/></center><br> +<center><title>Unguided Compare to ',opt$npcs,'</title><br><img src="unguided_npcs_',row,'.png"/></center><br> -<center><title>Guided Compare to ',opt$npcs,'</title><br><img src="guided_npcs.png"/></center><br> -<center><title>Unguided Compare to ',opt$npcs,'</title><br><img src="unguided_npcs.png"/></center><br> +<center><title>Guided Cumulative Variance</title><br><img src="guided_var_',row,'.png"/></center><br> +<center><title>Unguided Cumulative Variance</title><br><img src="unguided_var_',row,'.png"/></center><br> -<center><title>Guided Cumulative Variance</title><br><img src="guided_var.png"/></center><br> -<center><title>Unguided Cumulative Variance</title><br><img src="unguided_var.png"/></center><br> - -</html>' -),file = opt$html_outfile) +'), file = opt$html_outfile, append=TRUE) +} +write(paste('<p><center><a href="#top">Back to Top</a></center></p></body></html>'),file = opt$html_outfile, append=TRUE) sessionInfo()