Mercurial > repos > blankenberglab > gpca

comparison r-gpca.R @ 2:4865e7f4e9c5 draft

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planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit b72f398663cc133523cae0f5d7db2af1b4312f7a
author blankenberglab
date Tue, 27 Nov 2018 12:29:58 -0500
parents d93629e79f5e
children 8def7dda3bee
comparison
equal deleted inserted replaced
1:d93629e79f5e 2:4865e7f4e9c5
108 108
109 dir.create(opt$path); 109 dir.create(opt$path);
110 data<-t(as.matrix(read.delim(opt$data, row.names=1, header=TRUE, sep="\t"))) 110 data<-t(as.matrix(read.delim(opt$data, row.names=1, header=TRUE, sep="\t")))
111 batch<-as.matrix(read.delim(opt$batch, header=TRUE, row.names=1, sep="\t")) 111 batch<-as.matrix(read.delim(opt$batch, header=TRUE, row.names=1, sep="\t"))
112 112
113 write('<html><body><a name="top"></a>',file = opt$html_outfile, append=TRUE)
114 write('#Batch\tDelta\tP-value\tCumulative Variance',file = opt$numbers_outfile, append=TRUE) 113 write('#Batch\tDelta\tP-value\tCumulative Variance',file = opt$numbers_outfile, append=TRUE)
115 write('<div align="left><ul id =""><p><b>Table of Contents</b></p></ul></div>', file=opt$html_outfile, append=TRUE)
116 114
115 write('<html><body><div align="left" id="top"><p><h1>Table of Contents</h1><ul>',file = opt$html_outfile, append=TRUE)
117 for (row in 1:nrow(batch)) { 116 for (row in 1:nrow(batch)) {
118 write(paste0('<li><a href="#',row.names(batch)[row],'">',row.names(batch)[row],'</a></li>'), file=opt$html_outfile, append=TRUE) 117 write(paste0('<li><a href="#',row.names(batch)[row],'">',row.names(batch)[row],'</a></li>'), file=opt$html_outfile, append=TRUE)
119 } 118 }
119 write('</ul></p></div>', file=opt$html_outfile, append=TRUE)
120
120 for (row in 1:nrow(batch)) { 121 for (row in 1:nrow(batch)) {
121 batch1<-as.numeric(factor(batch[row,])) 122 batch1<-as.numeric(factor(batch[row,]))
122 123
123 out<-gPCA.batchdetect(x=data, batch=batch1, center=opt$center, scaleY=opt$scaleY, nperm=opt$nperm, filt=opt$filt, seed=opt$seed) 124 out<-gPCA.batchdetect(x=data, batch=batch1, center=opt$center, scaleY=opt$scaleY, nperm=opt$nperm, filt=opt$filt, seed=opt$seed)
124 125