diff r-gpca.R @ 0:ed24bacaa4d0 draft

planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit ec2f585063522efa001e4d2a639e92a67758ad8c-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/r-gpca.R	Mon Nov 19 10:15:19 2018 -0500
@@ -0,0 +1,186 @@
+#!/usr/bin/env Rscript 
+library(optparse)
+library(gPCA)
+
+
+# parse options
+option_list = list(
+   make_option(
+    c("--version"),
+    action = "store_true",
+    default = FALSE,
+    help = "Print version and exit"
+   ),
+  make_option(
+    c("-i", "--batch"),
+    action = "store",
+    default = NA,
+    type = 'character',
+    help = "Input batch"
+  ),
+  make_option(
+    c("-d", "--data"),
+    action = "store",
+    default = NA,
+    type = 'character',
+    help = "Input data"
+  ),
+   make_option(
+    c("-n", "--nperm"),
+    action = "store",
+    default = 1000,
+    type = 'numeric',
+    help = "Number of permutations to preform"
+   ),
+   make_option(
+    c("-c", "--center"),
+    action = "store_true",
+    default = FALSE,
+    help = "Is the input batch and data centered [default %default]"
+	 ),
+   make_option(
+    c("-y", "--scaleY"),
+    action = "store_true",
+    default = FALSE,
+    help = "Scale to Y axis"
+   ),
+   make_option(
+    c("-f", "--filt"),
+    action = "store",
+    default = NULL,
+    type = 'numeric',
+    help = "Retain features"
+	 ),
+   make_option(
+    c( "--npcs"),
+    action = "store",
+    default = 3,
+    type = 'numeric',
+    help = "Number of principal components to plot"
+   ),
+   make_option(
+    c("-p", "--path"),
+    action = "store",
+    default = '$html_outfile.extra_files_path', 
+    type = 'character',
+    help = "File path"
+   ),
+   make_option(
+    c("-s", "--seed"),
+    action = "store",
+    default = NULL,
+    type = 'numeric',
+    help = "Set a seed number"
+   ),
+   make_option(
+    c("-x", "--numbers_outfile"),
+    action = "store",
+    default = NA, 
+    type = 'character',
+    help = "Numbers output"
+ 	 ),
+   make_option(
+    c("-o", "--html_outfile"),
+    action = "store",
+    default = NA,
+    type = 'character',
+    help = "Output",
+  )
+)
+
+opt <-parse_args(OptionParser(option_list = option_list))
+
+if (opt$version){
+  # print version and exit
+  cat(paste("gPCA version", toString(packageVersion("gPCA"))), "\n")
+  quit()
+}
+
+# Check parameter values
+
+if ( ! file.exists(opt$batch)){
+  stop((paste('File for batch', opt$batch, 'does not exist')))
+}
+if ( ! file.exists(opt$data)){
+  stop((paste('File for data', opt$data, 'does not exist')))
+}
+
+batch<-as.numeric(factor(as.matrix(read.delim(opt$batch, header=TRUE, row.names=1, sep="\t"))))
+
+data<-t(as.matrix(read.delim(opt$data, row.names=1, header=TRUE, sep="\t")))
+
+out<-gPCA.batchdetect(x=data, batch=batch, 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)
+
+# General Distribution 
+par(mai=c(0.8,0.8,0.1,0.1),cex=0.8)
+png(paste(opt$path,'/gDist.png', sep=""), width=1020, height=800, units='px')
+gDist(out)
+invisible(dev.off())
+
+
+# Guided/Unguided 1v2
+par(mai=c(0.8,0.8,0.1,0.1),cex=0.8)
+png(paste(opt$path,'/guided_1v2.png', sep=""), width=1020, height=800, units='px')
+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$path,'/unguided_1v2.png', sep=""), width=1020, height=800, units='px')
+PCplot(out,ug="unguided",type="1v2")
+invisible(dev.off())
+
+
+# Guided/Unguided comp,3
+par(mai=c(0.65,0.65,0.1,0.1),cex=0.8)
+png(paste(opt$path,'/guided_npcs.png', sep=""), width=1020, height=800, units='px')
+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')
+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')
+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$path,'/unguided_var.png', sep=""), width=1020, height=800, units='px')
+CumulativeVarPlot(out,ug="unguided",col="blue")
+invisible(dev.off())
+
+
+write(paste('<html>
+<table id="r-gpca-wrap" align="center" border="1">
+ <tr>
+  <th>Delta</th><th>P-value</th><th>varPCg1</th>
+ </tr>
+ <tr>
+  <td id=delta>',out$delta,'</td><td id=p.val>',out$p.val,'</td><td id=varPCg1>',out$varPCg1,'</td>
+ </tr>
+</table>
+
+<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$npcs,'</title><br><img src="guided_npcs.png"/></center><br>
+<center><title>Unguided Compare to ',opt$npcs,'</title><br><img src="unguided_npcs.png"/></center><br>
+
+<center><title>Guided Cumulative Variance</title><br><img src="guided_var.png"/></center><br>
+<center><title>Unguided Cumulative Variance</title><br><img src="unguided_var.png"/></center><br>
+
+</html>'
+),file = opt$html_outfile)
+
+sessionInfo()