# HG changeset patch
# User blankenberglab
# Date 1543334566 18000
# Node ID d93629e79f5edcb5da7b928b3660a9d3919ac6cc
# Parent ed24bacaa4d00ca4934ba5a49ffc332d80392070
planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit 3b791d44853d8928046914cd93112bdcf89d4965
diff -r ed24bacaa4d0 -r d93629e79f5e r-gpca.R
--- 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('',file = opt$html_outfile, append=TRUE)
+write('#Batch\tDelta\tP-value\tCumulative Variance',file = opt$numbers_outfile, append=TRUE)
+write('', file=opt$html_outfile, append=TRUE)
+
+for (row in 1:nrow(batch)) {
+ write(paste0('',row.names(batch)[row],''), file=opt$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('
-
+write(paste0('
+',row.names(batch)[row],'
+
+
| Delta | P-value | varPCg1 |
- | ',out$delta,' | ',out$p.val,' | ',out$varPCg1,' |
+ ',out$delta,' | ',out$p.val,' | ',out$varPCg1,' |
+
+Guided 1v2
+Unguided 1v2
-
-Guided 1v2
-Unguided 1v2
+Guided Compare to ',opt$npcs,'
+Unguided Compare to ',opt$npcs,'
-Guided Compare to ',opt$npcs,'
-Unguided Compare to ',opt$npcs,'
+Guided Cumulative Variance
+Unguided Cumulative Variance
-Guided Cumulative Variance
-Unguided Cumulative Variance
-
-'
-),file = opt$html_outfile)
+'), file = opt$html_outfile, append=TRUE)
+}
+write(paste('Back to Top'),file = opt$html_outfile, append=TRUE)
sessionInfo()
diff -r ed24bacaa4d0 -r d93629e79f5e r-gpca.xml
--- a/r-gpca.xml Mon Nov 19 10:15:19 2018 -0500
+++ b/r-gpca.xml Tue Nov 27 11:02:46 2018 -0500
@@ -35,7 +35,7 @@
-
+
@@ -54,16 +54,43 @@
+
+
+
+
+
+
+
+
+
+
+
+
@@ -88,11 +115,20 @@
seed: the seed number for set.seed(). Default is NULL.
- Literature:
+ npcs: number of principal components to calculate
+
+ **Literature**
https://cran.r-project.org/web/packages/gPCA/gPCA.pdf
https://cran.r-project.org/web/packages/gPCA/vignettes/gPCA.pdf
+
+ **Input File Help**
+
+ Batch: The batch file must be a tab delimited file. It will be read as a numeric vector, consisting of as many different batches as you like. The test data file batch_in_multiple_1.tabular shows the correct format. The length of batch must conform to the data matrix or an error will occur.
+
+ Data: The data file must be a tab delimited file. It will be read in as a matrix. The test data file data_in_1.tabular shows the correct format. If you are receving errors about nonconformed matrices in your matrix you might need to transpose your matrix before using it in the tool.
+
]]>
diff -r ed24bacaa4d0 -r d93629e79f5e test-data/batch_in_multiple_1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/batch_in_multiple_1.tabular Tue Nov 27 11:02:46 2018 -0500
@@ -0,0 +1,3 @@
+#batch sample_1 sample_2 sample_3 sample_4 sample_5 sample_6 sample_7 sample_8 sample_9 sample_10
+time_period batch_1 batch_3 batch_3 batch_3 batch_2 batch_2 batch_1 batch_2 batch_3 batch_3
+random_batch b a c a a c b a c a
\ No newline at end of file
diff -r ed24bacaa4d0 -r d93629e79f5e test-data/html_outfile_1/gDist.png
Binary file test-data/html_outfile_1/gDist.png has changed
diff -r ed24bacaa4d0 -r d93629e79f5e test-data/html_outfile_1/gDist_1.png
Binary file test-data/html_outfile_1/gDist_1.png has changed
diff -r ed24bacaa4d0 -r d93629e79f5e test-data/html_outfile_1/guided_1v2.png
Binary file test-data/html_outfile_1/guided_1v2.png has changed
diff -r ed24bacaa4d0 -r d93629e79f5e test-data/html_outfile_1/guided_1v2_1.png
Binary file test-data/html_outfile_1/guided_1v2_1.png has changed
diff -r ed24bacaa4d0 -r d93629e79f5e test-data/html_outfile_1/guided_npcs.png
Binary file test-data/html_outfile_1/guided_npcs.png has changed
diff -r ed24bacaa4d0 -r d93629e79f5e test-data/html_outfile_1/guided_npcs_1.png
Binary file test-data/html_outfile_1/guided_npcs_1.png has changed
diff -r ed24bacaa4d0 -r d93629e79f5e test-data/html_outfile_1/guided_var.png
Binary file test-data/html_outfile_1/guided_var.png has changed
diff -r ed24bacaa4d0 -r d93629e79f5e test-data/html_outfile_1/guided_var_1.png
Binary file test-data/html_outfile_1/guided_var_1.png has changed
diff -r ed24bacaa4d0 -r d93629e79f5e test-data/html_outfile_1/html_outfile_1.html
--- a/test-data/html_outfile_1/html_outfile_1.html Mon Nov 19 10:15:19 2018 -0500
+++ b/test-data/html_outfile_1/html_outfile_1.html Tue Nov 27 11:02:46 2018 -0500
@@ -1,21 +1,26 @@
-
-
