diff tools/script.R @ 0:c5a812cdf478 draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/script.R	Fri Dec 09 10:52:35 2016 -0500
@@ -0,0 +1,68 @@
+#!/usr/bin/env Rscript
+
+args = commandArgs(TRUE)
+countDataPath = args[1]
+statsDataPath = args[2]
+logFC = args[3]
+logCPM = args[4]
+pValue = args[5]
+fdr = args[6]
+
+require(preprocessCore)
+require(gplots)
+
+#prepare counts data --------------------------------------------------------
+countData = read.table(countDataPath, comment = "",
+                       sep = "\t")
+
+groups = sapply(as.character(countData[1, -1]), strsplit, ":")
+groups = as.vector(t(countData[1, -1]))
+
+names = as.vector(t(countData[2, -1]))
+
+countData = countData[-c(1,2), ]
+rownames(countData) = countData[, 1]
+countData = countData[, -1]
+colnames(countData) = names
+
+countData = countData[, order(groups, names)]
+
+# prepare stats data ------------------------------------------------------
+
+statsData = read.table(statsDataPath, sep = "\t",
+                       header = T)
+
+colnames(statsData)[-1] = sapply(colnames(statsData)[-1], function(x){
+  unlist(strsplit(x, ".", fixed = T))[3]
+})
+
+wh = which(abs(statsData$logFC) >= logFC & statsData$logCPM >= logCPM & statsData$PValue <= pValue & statsData$FDR <= fdr)
+
+for(i in 1:ncol(countData)){
+  countData[,i] = as.numeric(countData[,i])
+}
+
+countDataNorm = normalize.quantiles(as.matrix(countData), copy = T)
+countDataNormLog = log(countDataNorm + 1, 2)
+
+colnames(countDataNormLog) = colnames(countData)
+rownames(countDataNormLog) = rownames(countData)
+
+#svg("heatmap.svg", width = 3+length(names), height = 1/2*length(wh))
+pdf("heatmap.pdf")
+
+heatmap.2(
+  countDataNormLog[wh, ],
+  density.info=c("none"),
+  hclustfun = function(x) hclust(x, method = "average"),
+  distfun = function(x) as.dist(1-cor(t(x))),  
+  col = bluered(50), 
+  scale = 'row', 
+  trace = "none", #lwid = c(1, length(names)),  lhei = c(1,1/3*length(wh)),
+#  Rowv=NA, 
+  Colv = NA,
+  margins = c(7, 8)
+)
+
+dev.off()
+