Mercurial > repos > stef > qdnaseq

changeset 81:5eec30e0fcce draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author stef
date Thu, 28 May 2015 13:45:43 -0400
parents 67cbaa54fa03
children 60a73de54206
files QDNAseq-plot.R QDNAseq-plot.xml QDNAseq-version.R QDNAseq.xml
diffstat 4 files changed, 84 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/QDNAseq-plot.R	Fri May 08 05:59:20 2015 -0400
+++ b/QDNAseq-plot.R	Thu May 28 13:45:43 2015 -0400
@@ -37,11 +37,36 @@
 catMsg( c( rVersion ) )
 
 qdnaseqObject <- readRDS( rdsFilePath )
+chromosomesToPlot <- unlist( strsplit( chromosomesToPlotString, ",") )
+
+#cat( "CHROM: ", chromosomesToPlotString, "\n" )
+#cat( "REGION: ", regionToPlotString, "\n" )
+#cat( "What to plot: ", whatToPlot, "\n" )
+
 ## COPYNUMBER PLOT
 sample <- SAMPLE_INDEX
 png( outputPngPath, width=PLOT_WIDTH, height=PLOT_HEIGHT, res=PLOT_RES )
 	par( PAR_SET )
-	plot( qdnaseqObject[ ,sample ] ) 
+	if ( whatToPlot == 'everything' ){
+		catMsg( c( "Plotting all data in object" ) )
+		plot( qdnaseqObject[ ,sample ] ) 	
+	} else if( whatToPlot == 'chromosomes' ){
+		catMsg( c( "Plotting subset of chromosomes" ) )
+		fdata <- qdnaseqObject@featureData@data
+		idx_region <- which( fdata$chromosome %in% chromosomesToPlot )
+		plot( qdnaseqObject[ idx_region, sample ] ) 		
+	} else if( whatToPlot == 'region' ){
+		regionC <- chrName
+		regionS <- chrStart
+		regionE <- chrEnd
+		if ( regionS > regionE ) stop("Chosen start is > end")
+		catMsg( c( "Plotting genomic region (chr=", regionC, " start=", regionS, " end=", regionE, ")" ) )
+		
+		fdata <- qdnaseqObject@featureData@data
+		idx_region <- which( fdata$chromosome == regionC & fdata$start > regionS & fdata$end < regionE )
+		
+		plot( qdnaseqObject[ idx_region, sample ], doCalls=FALSE ) 		
+	}
 	#mtext( "plotted in galaxy", 3 )
 	abline( h=c(-2,-1,1,2,3,4), lty=1, lwd=0.5, col="grey" )
 dev.off()
--- a/QDNAseq-plot.xml	Fri May 08 05:59:20 2015 -0400
+++ b/QDNAseq-plot.xml	Thu May 28 13:45:43 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="QDNAseq-plot" name="QDNAseq-plot" version="0.0.1" force_history_refresh="True">
+<tool id="QDNAseq-plot" name="QDNAseq-plot" version="0.0.2" force_history_refresh="True">
   
   <requirements>
     
@@ -16,6 +16,8 @@
     $cfg
   </command>
 
+  <version_command interpreter="Rscript">QDNAseq-version.R</version_command>
+
   <stdio>
     <!-- Anything higher than 0 means the R script didnt finish (correctly) -->
     <!-- Because different R packages deal with err/warn differently unable to waterproof this -->
@@ -57,7 +59,53 @@
       
     </conditional> 
     -->
-    <param name="sample_index" type="integer" required="True" value="1" label="Sample-index (integer)" help="The RDS input object can contain data from multiple individuals, this number tells the script which one to plot. Plotting multiple at the same time is not supported." />
+    <param name="sample_index" type="integer" required="True" value="1" label="Sample-index (integer)" help="The RDS input object can contain data from multiple samples, this index tells the script which one to plot. Plotting multiple samples at the same time is not supported." />
+
+    <conditional name="subset_selection">
+      <param name="what_to_plot" type="select" label="What to plot" help="Instead of plotting everything in the object you can also select certain chromosomes or set a genomic region">
+        <option value="all">Everything</option>
+        <option value="chromosomes">Selected chromosomes</option>
+        <option value="region">Genomic region</option>
+      </param>
+      <when value="all">
+        <!-- ==================== -->
+      </when>
+      <when value="chromosomes">
+        <!-- ==================== -->
+        <param name="chromosomes" type="select" multiple="true" optional="false" label="Select chromosomes to plot" help="To zoom in on a particular chromosome you can select one or more here">
+          <option value="1">1</option><option value="2">2</option>
+          <option value="3">3</option><option value="4">4</option>
+          <option value="5">5</option><option value="6">6</option>
+          <option value="7">7</option><option value="8">8</option>
+          <option value="9">9</option><option value="10">10</option>
+          <option value="11">11</option><option value="12">12</option>
+          <option value="13">13</option><option value="14">14</option>
+          <option value="15">15</option><option value="16">16</option>
+          <option value="17">17</option><option value="18">18</option>
+          <option value="19">19</option><option value="20">20</option>
+          <option value="21">21</option><option value="22">22</option>
+          <!--<option value="X" selected="true">X</option>-->
+          <!--<option value="Y" selected="true">Y</option>-->
+        </param>
+        <param name="chr_name" type="hidden" value="NA" />
+        <param name="chr_start" type="hidden" value="NA" />
+        <param name="chr_end" type="hidden" value="NA" />
+      </when>
+      <when value="region">
+        <!-- ==================== -->
+        <!--
+        <param name="genomic_region" type="text" optional="false" label="Genomic region" help="Supply a genomic region in format chr1:12345-23456" value="chr1:12345-23456" size="30">
+          <validator type="regex" message="No whitespace characters allowed">^[^\s\\]*$</validator>
+          <validator type="regex" message="String is not of correct format">^chr\d+\:\d+\-\d+$</validator>
+        </param>
+        -->
+        <param name="chr_name" size="2" type="integer" optional="false" value="" label="Chromosome" />
+        <param name="chr_start" size="15" type="integer" optional="false" value="" label="Start position on chromosome" />
+        <param name="chr_end" size="15" type="integer" optional="false" value="" label="End position on chromosome" />
+        <param name="chromosomes" type="hidden" value="NA" />
+      </when>
+
+    </conditional>
 
     <!-- ==================== -->
     <!-- Optional advanced options -->
@@ -98,6 +146,11 @@
 "${outputPng}" -> outputPngPath
 "${rdsFile}" -> rdsFilePath
 as.integer( "${sample_index}" ) -> SAMPLE_INDEX
+"${subset_selection.what_to_plot}" -> whatToPlot
+"${subset_selection.chromosomes}" -> chromosomesToPlotString
+"${subset_selection.chr_name}" -> chrName
+"${subset_selection.chr_start}" -> chrStart
+"${subset_selection.chr_end}" -> chrEnd
 
 ## -----
 ## extra options
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/QDNAseq-version.R	Thu May 28 13:45:43 2015 -0400
@@ -0,0 +1,1 @@
+cat( packageDescription("QDNAseq", fields = "Version") )
\ No newline at end of file
--- a/QDNAseq.xml	Fri May 08 05:59:20 2015 -0400
+++ b/QDNAseq.xml	Thu May 28 13:45:43 2015 -0400
@@ -19,6 +19,8 @@
     \$QDNASEQ_PATH
   </command>
 
+  <version_command interpreter="Rscript">QDNAseq-version.R</version_command>
+
   <stdio>
     <!-- Anything higher than 0 means the R script didnt finish (correctly) -->
     <!-- Because different R packages deal with err/warn differently unable to waterproof this -->