# HG changeset patch
# User davidvanzessen
# Date 1400160654 14400
# Node ID b850200d43350380a01fe000a3cfdb8cc521e11f
# Parent fd1b7681639528af0414d0a5af25b91f9a0155d9
Uploaded
diff -r fd1b76816395 -r b850200d4335 RScript.r
--- a/RScript.r Thu Mar 27 10:54:03 2014 -0400
+++ b/RScript.r Thu May 15 09:30:54 2014 -0400
@@ -6,6 +6,9 @@
outFile = args[2]
outDir = args[3]
clonalType = args[4]
+species = args[5]
+locus = args[6]
+selection = args[7]
if (!("gridExtra" %in% rownames(installed.packages()))) {
install.packages("gridExtra", repos="http://cran.xl-mirror.nl/")
@@ -63,7 +66,9 @@
PRODF$freq = as.numeric(PRODF$freq)
} else {
PRODF$freq = 1
- PRODF = PRODF[!duplicated(PRODF$VDJCDR3), ]
+ if(selection == "unique"){
+ PRODF = PRODF[!duplicated(PRODF$VDJCDR3), ]
+ }
}
PRODFV = data.frame(data.table(PRODF)[, list(Length=sum(freq)), by=c("Sample", "Top.V.Gene")])
@@ -87,20 +92,55 @@
PRODFJ = merge(PRODFJ, Total, by.x='Sample', by.y='Sample', all.x=TRUE)
PRODFJ = ddply(PRODFJ, c("Sample", "Top.J.Gene"), summarise, relFreq= (Length*100 / Total))
-V = c("v.name\tchr.orderV\nTRBV1\t1\nTRBV2\t2\nTRBV3\t3\nTRBV4\t4\nTRBV5\t5\nTRBV12-1\t6\nTRBV13-1\t7\nTRBV12-2\t8\nTRBV13-2\t9\nTRBV13-3\t10\nTRBV14\t11\nTRBV15\t12\nTRBV16\t13\nTRBV17\t14\nTRBV19\t15\nTRBV20\t16\nTRBV23\t17\nTRBV24\t18\nTRBV26\t19\nTRBV29\t20\nTRBV30\t21\nTRBV31\t22\n")
+V = c("v.name\tchr.orderV\n")
+D = c("v.name\tchr.orderD\n")
+J = c("v.name\tchr.orderJ\n")
+
+if(species == "human"){
+ if(locus == "trb"){
+ V = c("v.name\tchr.orderV\nTRBV2\t1\nTRBV3-1\t2\nTRBV4-1\t3\nTRBV5-1\t4\nTRBV6-1\t5\nTRBV4-2\t6\nTRBV6-2\t7\nTRBV4-3\t8\nTRBV6-3\t9\nTRBV7-2\t10\nTRBV6-4\t11\nTRBV7-3\t12\nTRBV9\t13\nTRBV10-1\t14\nTRBV11-1\t15\nTRBV10-2\t16\nTRBV11-2\t17\nTRBV6-5\t18\nTRBV7-4\t19\nTRBV5-4\t20\nTRBV6-6\t21\nTRBV5-5\t22\nTRBV7-6\t23\nTRBV5-6\t24\nTRBV6-8\t25\nTRBV7-7\t26\nTRBV6-9\t27\nTRBV7-8\t28\nTRBV5-8\t29\nTRBV7-9\t30\nTRBV13\t31\nTRBV10-3\t32\nTRBV11-3\t33\nTRBV12-3\t34\nTRBV12-4\t35\nTRBV12-5\t36\nTRBV14\t37\nTRBV15\t38\nTRBV16\t39\nTRBV18\t40\nTRBV19\t41\nTRBV20-1\t42\nTRBV24-1\t43\nTRBV25-1\t44\nTRBV27\t45\nTRBV28\t46\nTRBV29-1\t47\nTRBV30\t48")
+ D = c("v.name\tchr.orderD\nTRBD1\t1\nTRBD2\t2\n")
+ J = c("v.name\tchr.orderJ\nTRBJ1-1\t1\nTRBJ1-2\t2\nTRBJ1-3\t3\nTRBJ1-4\t4\nTRBJ1-5\t5\nTRBJ1-6\t6\nTRBJ2-1\t7\nTRBJ2-2\t8\nTRBJ2-3\t9\nTRBJ2-4\t10\nTRBJ2-5\t11\nTRBJ2-6\t12\nTRBJ2-7\t13")
+ } else if (locus == "tra"){
+ V = c("v.name\tchr.orderVTRAV1-1\t1\nTRAV1-2\t2\nTRAV2\t3\nTRAV3\t4\nTRAV4\t5\nTRAV5\t6\nTRAV6\t7\nTRAV7\t8\nTRAV8-1\t9\nTRAV9-1\t10\nTRAV10\t11\nTRAV12-1\t12\nTRAV8-2\t13\nTRAV8-3\t14\nTRAV13-1\t15\nTRAV12-2\t16\nTRAV8-4\t17\nTRAV13-2\t18\nTRAV14/DV4\t19\nTRAV9-2\t20\nTRAV12-3\t21\nTRAV8-6\t22\nTRAV16\t23\nTRAV17\t24\nTRAV18\t25\nTRAV19\t26\nTRAV20\t27\nTRAV21\t28\nTRAV22\t29\nTRAV23/DV6\t30\nTRAV24\t31\nTRAV25\t32\nTRAV26-1\t33\nTRAV27\t34\nTRAV29/DV5\t35\nTRAV30\t36\nTRAV26-2\t37\nTRAV34\t38\nTRAV35\t39\nTRAV36/DV7\t40\nTRAV38-1\t41\nTRAV38-2/DV8\t42\nTRAV39\t43\nTRAV40\t44\nTRAV41\t45\n")
+ D = c("v.name\tchr.orderD\n")
+ J = c("v.name\tchr.orderJ\nTRAJ57\t1\nTRAJ56\t2\nTRAJ54\t3\nTRAJ53\t4\nTRAJ52\t5\nTRAJ50\t6\nTRAJ49\t7\nTRAJ48\t8\nTRAJ47\t9\nTRAJ46\t10\nTRAJ45\t11\nTRAJ44\t12\nTRAJ43\t13\nTRAJ42\t14\nTRAJ41\t15\nTRAJ40\t16\nTRAJ39\t17\nTRAJ38\t18\nTRAJ37\t19\nTRAJ36\t20\nTRAJ34\t21\nTRAJ33\t22\nTRAJ32\t23\nTRAJ31\t24\nTRAJ30\t25\nTRAJ29\t26\nTRAJ28\t27\nTRAJ27\t28\nTRAJ26\t29\nTRAJ24\t30\nTRAJ23\t31\nTRAJ22\t32\nTRAJ21\t33\nTRAJ20\t34\nTRAJ18\t35\nTRAJ17\t36\nTRAJ16\t37\nTRAJ15\t38\nTRAJ14\t39\nTRAJ13\t40\nTRAJ12\t41\nTRAJ11\t42\nTRAJ10\t43\nTRAJ9\t44\nTRAJ8\t45\nTRAJ7\t46\nTRAJ6\t47\nTRAJ5\t48\nTRAJ4\t49\nTRAJ3\t50")
+ } else if (locus == "trg"){
+ cat("human trg not yet implemented")
+ } else if (locus == "trd"){
+ cat("human trd not yet implemented")
+ }
+} else if (species == "mouse"){
+ if(locus == "trb"){
+ cat("mouse trb not yet implemented")
+ } else if (locus == "tra"){
+ cat("mouse tra not yet implemented")
+ } else if (locus == "trg"){
+ cat("mouse trg not yet implemented")
+ } else if (locus == "trd"){
+ cat("mouse trd not yet implemented")
+ }
+}
+useD = TRUE
+if(species == "human" && locus == "tra"){
+ useD = FALSE
+ cat("No D Genes in this species/locus")
+}
+
+
tcV = textConnection(V)
Vchain = read.table(tcV, sep="\t", header=TRUE)
PRODFV = merge(PRODFV, Vchain, by.x='Top.V.Gene', by.y='v.name', all.x=TRUE)
close(tcV)
-D = c("v.name\tchr.orderD\nTRBD1\t1\nTRBD2\t2\n")
+
tcD = textConnection(D)
Dchain = read.table(tcD, sep="\t", header=TRUE)
PRODFD = merge(PRODFD, Dchain, by.x='Top.D.Gene', by.y='v.name', all.x=TRUE)
close(tcD)
-J = c("v.name\tchr.orderJ\nTRBJ1-1\t1\nTRBJ1-2\t2\nTRBJ1-3\t3\nTRBJ1-4\t4\nTRBJ1-5\t5\nTRBJ2-1\t6\nTRBJ2-2\t7\nTRBJ2-3\t8\nTRBJ2-4\t9\nTRBJ2-5\t10\nTRBJ2-6\t11\nTRBJ2-7\t12\n")
+
tcJ = textConnection(J)
Jchain = read.table(tcJ, sep="\t", header=TRUE)
PRODFJ = merge(PRODFJ, Jchain, by.x='Top.J.Gene', by.y='v.name', all.x=TRUE)
@@ -201,6 +241,7 @@
revVchain$chr.orderV = rev(revVchain$chr.orderV)
revDchain$chr.orderD = rev(revDchain$chr.orderD)
+
plotVD <- function(dat){
if(length(dat[,1]) == 0){
return()
@@ -236,8 +277,6 @@
lapply(VDList, FUN=plotVD)
-
-
plotVJ <- function(dat){
if(length(dat[,1]) == 0){
return()
@@ -304,7 +343,6 @@
DJList = split(completeDJ, f=completeDJ[,"Sample"])
lapply(DJList, FUN=plotDJ)
-
sampleFile <- file("samples.txt")
un = unique(test$Sample)
un = paste(un, sep="\n")
diff -r fd1b76816395 -r b850200d4335 plotting_merged.xml
--- a/plotting_merged.xml Thu Mar 27 10:54:03 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,23 +0,0 @@
-
-
-
- r_wrapper.sh $in_file $out_file $out_file.files_path "$clonaltype_select"
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- Step 4 of the Immune Repertoire tools, plots the merged data, generating 3 bar charts for V, D and J frequencies and 3 heatmaps for every sample (V-D, V-J, D-J)
-
-
diff -r fd1b76816395 -r b850200d4335 r_wrapper.sh
--- a/r_wrapper.sh Thu Mar 27 10:54:03 2014 -0400
+++ b/r_wrapper.sh Thu May 15 09:30:54 2014 -0400
@@ -4,9 +4,16 @@
outputDir=$3
outputFile=$3/index.html #$2
clonalType=$4
+species=$5
+locus=$6
+selection=$7
+useD="true"
+if [[ "$species" == "human" && "$locus" = "tra" ]] ; then
+ useD="false"
+fi
dir="$(cd "$(dirname "$0")" && pwd)"
mkdir $3
-Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType 2>&1
+Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType $species $locus $selection 2>&1
cp $dir/tabber.js $outputDir
cp $dir/style.css $outputDir
cp $dir/script.js $outputDir
@@ -26,10 +33,14 @@
echo "
" >> $outputFile
echo "
" >> $outputFile
-echo "
" >> $outputFile
+if [[ "$useD" == "true" ]] ; then
+ echo "" >> $outputFile
+fi
echo "
" >> $outputFile
echo "
" >> $outputFile
-echo "
" >> $outputFile
+if [[ "$useD" == "true" ]] ; then
+ echo "" >> $outputFile
+fi
echo "
" >> $outputFile
samples=`cat $outputDir/samples.txt`
@@ -37,9 +48,14 @@
echo "" >> $outputFile
count=$((count+1))
done
echo "
| The dataset used to generate the CDR3 length frequency graph | Download |
" >> $outputFile
echo "| The dataset used to generate the V gene family frequency graph | Download |
" >> $outputFile
-echo "| The dataset used to generate the D gene family frequency graph | Download |
" >> $outputFile
+if [[ "$useD" == "true" ]] ; then
+ echo "| The dataset used to generate the D gene family frequency graph | Download |
" >> $outputFile
+fi
echo "| The dataset used to generate the J gene family frequency graph | Download |
" >> $outputFile
echo "| The dataset used to generate the V gene frequency graph | Download |
" >> $outputFile
-echo "| The dataset used to generate the D gene frequency graph | Download |
" >> $outputFile
+if [[ "$useD" == "true" ]] ; then
+ echo "| The dataset used to generate the D gene frequency graph | Download |
" >> $outputFile
+fi
echo "| The dataset used to generate the J gene frequency graph | Download |
" >> $outputFile
for sample in $samples; do
- echo "| The data used to generate the VD heatmap for $sample. | Download |
" >> $outputFile
+ if [[ "$useD" == "true" ]] ; then
+ echo "| The data used to generate the VD heatmap for $sample. | Download |
" >> $outputFile
+ fi
echo "| The data used to generate the VJ heatmap for $sample. | Download |
" >> $outputFile
- echo "| The data used to generate the DJ heatmap for $sample. | Download |
" >> $outputFile
+ if [[ "$useD" == "true" ]] ; then
+ echo "| The data used to generate the DJ heatmap for $sample. | Download |
" >> $outputFile
+ fi
done
echo "" >> $outputFile
diff -r fd1b76816395 -r b850200d4335 report_tcell.xml
--- a/report_tcell.xml Thu Mar 27 10:54:03 2014 -0400
+++ b/report_tcell.xml Thu May 15 09:30:54 2014 -0400
@@ -1,7 +1,7 @@
- r_wrapper.sh $in_file $out_file $out_file.files_path "$clonaltype_select" "$species"
+ r_wrapper.sh $in_file $out_file $out_file.files_path "$clonaltype_select" $species $locus $selection
@@ -12,10 +12,23 @@
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
