[Qpcr-commits] r106 - pkg/NormqPCR/R

[noreply at r-forge.r-project.org]

Author: jperkins
Date: 2010-05-17 19:10:29 +0200 (Mon, 17 May 2010)
New Revision: 106

Added:
   pkg/NormqPCR/R/plotDdCt.R
Log:
barplots..getting very random behaviour for the error bars

Added: pkg/NormqPCR/R/plotDdCt.R
===================================================================
--- pkg/NormqPCR/R/plotDdCt.R	                        (rev 0)
+++ pkg/NormqPCR/R/plotDdCt.R	2010-05-17 17:10:29 UTC (rev 106)
@@ -0,0 +1,51 @@
+#library(gplots)
+plotDdCt <- function(qPCRSet, ddCtTable, detectors="", logFC = FALSE) {
+#	no.plots <- length(detectors)
+cat("start")
+#cat(eval(samples))
+
+#expM
+
+if(detectors!="") {
+#cat("WEN")
+    bbb <- ddCtTable[ddCtTable$ID %in% detectors,]
+    qPCRSet <- qPCRSet[detectors]
+#    expM <- matrix(exprs(qPCRSet)[detectors,], ncol=8)
+#    rownames(expM) <- detectors
+    expM <- exprs(qPCRSet)
+} else {
+cat("try")
+    bbb <- ddCtTable
+    expM <- exprs(qPCRSet)
+}
+cat("out")
+#print(bbb)
+cat("YEAH")
+ddCts <- as.vector(bbb$ddCt)
+ddCtsNames <- as.vector(bbb$ID)
+ddCtsMax <- log2(as.numeric(as.vector(bbb$ddCt.max)))
+ddCtsMin <- log2(as.numeric(as.vector(bbb$ddCt.min)))
+
+maxo <- ceiling(max(ddCtsMax,na.rm=T))
+mino <- floor(min(ddCtsMin,na.rm=T))
+nonNAs.back <- log2(as.numeric(ddCts))
+nonNAs.back[ddCts == "+"] <- maxo
+nonNAs.back[ddCts == "-"] <- mino
+ddCts <- nonNAs.back
+op <- par(las=2)
+bp <- barplot2(ddCts, plot.ci=TRUE, ci.l=ddCtsMin, ci.u=ddCtsMax, names.arg=ddCtsNames, ylab=expression("Fold change relative to control ("~Delta~Delta~"Cti)"))
+par(op)
+#for(i in rownames(qq)) { t<-c(t,(ww[i,]));points(rep(j[m],4),ww[i,]);m=m+1 }   
+#qq <- qPCRSet
+#cat("bbbbbbl")
+#return(expM)
+expM <- log2(expM)[,c(3:4,7:8)] - log2(expM)[,c(1:2,5:6)]
+if(length(detectors) == 1) expM <- matrix(expM, ncol=4)
+#cat(featureNames(qPCRSet))
+#rownames(expM) <- featureNames(qPCRSet)
+#print(expM)
+#return(expM)
+source("/home/bsm/jperkins/qpcr/pkg/NormqPCR/R/plotDdCt.R")
+j<-1; for(i in 1:length(featureNames(qPCRSet))) {cat(i);cat(bp[j]);print(expM[i,]); points(rep(bp[j],4),expM[i,]);j=j+1 }
+
+}