From 0eba687ce35279cf9ebdb8bcf1068c54436fd9cb Mon Sep 17 00:00:00 2001
From: kohleman <kohleman>
Date: Wed, 22 Jan 2014 16:14:36 +0000
Subject: [PATCH] -added pattern parameter - write numbers of bars in the
middle, more robust against small or huge differences in frequencies -renamed
variables
SVN: 30417
---
.../source/R/barcodeDistribution.R | 38 ++++++++++++-------
1 file changed, 25 insertions(+), 13 deletions(-)
diff --git a/deep_sequencing_unit/source/R/barcodeDistribution.R b/deep_sequencing_unit/source/R/barcodeDistribution.R
index ff665ca682e..33b7a9c2670 100644
--- a/deep_sequencing_unit/source/R/barcodeDistribution.R
+++ b/deep_sequencing_unit/source/R/barcodeDistribution.R
@@ -4,11 +4,15 @@ library("ShortRead")
args <- commandArgs(TRUE)
print(args)
path <- (args[1])
-path <- "/Users/kohleman/PycharmProjects/qgf/barcodeDistribution/testData"
-filenames <- list.files(path, pattern="lane6", full.names=TRUE)
+flowcell <- (args[2])
+pattern <- (args[3])
+#flowcell <- "C3CFPACXX"
+#path <- "/Users/kohleman/PycharmProjects/qgf/barcodeDistribution/testData"
+#pattern <- 'lane4'
+filenames <- list.files(path, pattern=pattern, full.names=TRUE)
totalIndexList <- ""
-plotTopIndices <- function (topIndices, xName="") {
+plotTopIndices <- function (topIndices, xName="", path) {
# Creates a barplot out of a data frame.
#
@@ -19,7 +23,11 @@ plotTopIndices <- function (topIndices, xName="") {
#
# Returns:
# an image/ a pdf
-
+
+ fileName <- (paste(xName,".pdf", sep=""))
+ fileFullPath <- (file.path(path, fileName))
+
+ pdf(file=fileFullPath)
par(mfcol=c(1, 1))
countLength<- nchar(toString(max(topIndices$Freq)))
@@ -28,7 +36,8 @@ plotTopIndices <- function (topIndices, xName="") {
b <- barplot(topIndices$Freq, main="Top 15 indices distribution", xlab=paste("Count of Indices for", xName), horiz=TRUE,
names=topIndices$totalIndexList, cex.names=.75, las=1)
- text(cex=.75, x=topIndices$Freq-(countLength * 2), y=b, labels=topIndices$Freq, xpd=TRUE)
+ text(cex=.75, x=topIndices$Freq/2, y=b, labels=topIndices$Freq, xpd=TRUE)
+ dev.off()
}
# -----------------------------------------------------------------------------
@@ -38,6 +47,9 @@ multmerge <- function(datalist, mergeBy){
Reduce(function(...) {merge(..., by = mergeBy, all=TRUE)}, datalist)
}
+# returns string w/o leading or trailing whitespace
+trim <- function (x) gsub("^\\s+|\\s+$", "", x)
+
# -----------------------------------------------------------------------------
streamFASTQ <- function (file, verbose = TRUE) {
@@ -82,20 +94,20 @@ if (length(ldf) > 1) {
list1 <- multmerge(ldf, "totalIndexList")
# Replacing all NAs with 0
list1 [is.na(list1)] <- 0
- # sum up the values row-wise for each column, but leave out the first and the
- # last column
- list1$Freq<- apply(list1[,c(-1,-length(list1))],1,sum)
+ # sum up the values row-wise for each column, but leave out the first column
+ list1$Freq<- apply(list1[,c(-1)],1,sum)
} else {
print ("Only one FASTQ found")
list1 <- ldf[[1]]
}
-ttt1 <- list1[c("totalIndexList","Freq")]
-orderedDf <- ttt1[with(ttt1, order(- Freq)), ]
+subList <- list1[c("totalIndexList","Freq")]
+orderedDf <- subList[with(subList, order(- Freq)), ]
topIndices <- orderedDf[1:15, ]
#print (topIndices)
-fileBaseName <- (basename(filenames[1]))
-plotTopIndices (topIndices, fileBaseName)
+fileBaseName <- paste(flowcell, unlist(strsplit(basename(filenames[1]), "_"))[1], sep="_")
+#fileBaseName <- trim(fileBaseName)
+plotTopIndices (topIndices, fileBaseName, path)
-#write.table(list1, file = "list1.csv", sep = ",", col.names = NA, qmethod = "double")
\ No newline at end of file
+#write.table(list1, file = "list1.csv", sep = ",", col.names = NA, qmethod = "double")
--
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