From 1d1a6256253f6a347f8dccfee70cde53d3b484fd Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 20 Jan 2016 14:49:53 +0100
Subject: [PATCH] Added heatmap plot
---
.../gentrap/measures/Measurement.scala | 28 +++++++++++++++----
1 file changed, 23 insertions(+), 5 deletions(-)
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/Measurement.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/Measurement.scala
index 351905676..d08b4ca42 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/Measurement.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/Measurement.scala
@@ -1,8 +1,11 @@
package nl.lumc.sasc.biopet.pipelines.gentrap.measures
+import java.io.File
+
import nl.lumc.sasc.biopet.core.Reference
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.extensions.tools.MergeTables
+import nl.lumc.sasc.biopet.pipelines.gentrap.scripts.PlotHeatmap
import org.broadinstitute.gatk.queue.QScript
/**
@@ -11,22 +14,32 @@ import org.broadinstitute.gatk.queue.QScript
trait Measurement extends SummaryQScript with Reference { qscript: QScript =>
protected var bamFiles: Map[String, File] = Map()
+ /**
+ * Method to add a bamFile to the pipeline
+ * @param id Uniqe id used for this bam file, most likly to be a sampleName
+ * @param file Location of the bam file
+ */
def addBamfile(id: String, file: File): Unit = {
require(!bamFiles.contains(id), s"'$id' already exist")
bamFiles += id -> file
}
+ /** Name of job, this is used as prefix for most of the files */
def name: String = this.getClass.getSimpleName.toLowerCase
+ /** Locations of single bam count tables */
lazy val countFiles: Map[String, File] = bamFiles.map { case (id, bamFile) => bamToCountFile(id, bamFile) }
+ /** Location of merge count table */
def mergedCountFile = new File(outputDir, s"$name.merged.tsv")
- case class MergeArgs(idCols: List[Int],
- valCol: Int,
- numHeaderLines: Int = 0,
- fallback: String = "-")
+ /** Location of heatmap */
+ def heatpMap = new File(outputDir, s"$name.heatmap.png")
+
+ /** Class to store args for MergeTables */
+ case class MergeArgs(idCols: List[Int], valCol: Int, numHeaderLines: Int = 0, fallback: String = "-")
+ /** This should contain the args for MergeTables */
def mergeArgs: MergeArgs
/** Init for pipeline */
@@ -39,9 +52,14 @@ trait Measurement extends SummaryQScript with Reference { qscript: QScript =>
add(MergeTables(this, countFiles.values.toList, mergedCountFile,
mergeArgs.idCols, mergeArgs.valCol, mergeArgs.numHeaderLines, mergeArgs.fallback))
- //TODO: Heatmap
+ val job = new PlotHeatmap(qscript)
+ job.input = mergedCountFile
+ job.output = heatpMap
+ job.countType = Some(name)
+ add(job)
}
+ /** This function should add the count table for each bamFile */
def bamToCountFile(id: String, bamFile: File): (String, File)
/** Must return a map with used settings for this pipeline */
--
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