# HG changeset patch
# User davidecangelosi
# Date 1559123938 14400
# Node ID 1e3113e565db31019e29ef8a5cc444a7d84a8fb8
# Parent  9227f7b1c50b1c4346cbd23bb5e0f90e16ca935e
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit f53b88658dc1aa6627b064d7c8bed1562dfbc1dc

diff -r 9227f7b1c50b -r 1e3113e565db pipe-t.R
--- 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!")
 )