Mercurial > repos > davidecangelosi > pipe_t
changeset 21:1e3113e565db draft
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit f53b88658dc1aa6627b064d7c8bed1562dfbc1dc
| author | davidecangelosi |
|---|---|
| date | Wed, 29 May 2019 05:58:58 -0400 |
| parents | 9227f7b1c50b |
| children | 822dc9b96b3e |
| files | pipe-t.R |
| diffstat | 1 files changed, 4 insertions(+), 2 deletions(-) [+] |
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--- a/pipe-t.R Tue May 28 06:53:43 2019 -0400 +++ b/pipe-t.R Wed May 29 05:58:58 2019 -0400 @@ -570,7 +570,7 @@ res = 300, # 300 pixels per inch pointsize = 8) - plotCtBoxes(xFilter, cex.lab=3, cex.axis = 2,stratify=NULL, xlab = "Samples", ylab="Ct", mar = c(8,8,8,8), names=as.character(seq(1, ncol(xFilter), 1))) # smaller font size + plotCtBoxes(xFilter, ylim=c(min(exprs(xFilter), na.rm = TRUE),max(exprs(xFilter), na.rm = TRUE)), cex.lab=3, cex.axis = 2,stratify=NULL, xlab = "Samples", ylab="Ct", mar = c(8,8,8,8), names=as.character(seq(1, ncol(xFilter), 1))) # smaller font size dev.off() #write.table(exprs(xFilter), file=x, quote=FALSE, row.names=TRUE, col.names=TRUE,sep = "\t") @@ -812,7 +812,7 @@ res = 300, # 300 pixels per inch pointsize = 8) - plotCtBoxes(normalizedDataset, cex.lab=3, cex.axis = 2,stratify=NULL, xlab = "Samples", ylab="DeltaCt", mar = c(8,8,8,8), names=as.character(seq(1, ncol(normalizedDataset), 1))) # smaller font size + plotCtBoxes(normalizedDataset, ylim=c(min(exprs(normalizedDataset), na.rm = TRUE),max(exprs(normalizedDataset),cex.lab=3, cex.axis = 2,stratify=NULL, xlab = "Samples", ylab="DeltaCt", mar = c(8,8,8,8), names=as.character(seq(1, ncol(normalizedDataset), 1))) # smaller font size dev.off() ################################################## Filtering based on number of NAs################################################## @@ -882,6 +882,8 @@ DEG<-RP(exprs(qFiltNAs), as.numeric(pData(qFiltNAs)$Treatment)-1, num.perm = 1000,logged = TRUE, gene.names = featureNames(qFiltNAs), huge=TRUE, plot = FALSE, rand = 123) write.table(DEG[1:5], file=outputDEA, quote=FALSE, row.names=TRUE, col.names=TRUE,sep = "\t") }, + "none"={ + }, stop("Enter something that switches me!") )