From 393af58430bddc053951705b43d641e17a09a3f0 Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Thu, 5 Mar 2015 17:25:12 +0100
Subject: [PATCH] Add heatmap plot jobs for all output
---
.../biopet/pipelines/gentrap/Gentrap.scala | 100 +++++++++++++-----
1 file changed, 74 insertions(+), 26 deletions(-)
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
index 799b07174..274c97510 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
@@ -108,56 +108,95 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
}
}
+ protected lazy val forTmmNormalization: Set[ExpMeasures.Value] =
+ Set(FragmentsPerGene, FragmentsPerExon, BasesPerGene, BasesPerExon)
+
+ private def makeHeatmapJob(mergeJob: Option[MergeTables], outName: String,
+ expMeasure: ExpMeasures.Value, isCuffIsoform: Boolean = false): Option[PlotHeatmap] =
+ (mergeJob.isDefined && samples.size > 2)
+ .option {
+ val job = new PlotHeatmap(qscript)
+ job.input = mergeJob.get.output
+ job.output = new File(outputDir, "heatmaps" + File.separator + s"heatmap_$outName.png")
+ job.tmmNormalize = forTmmNormalization.contains(expMeasure)
+ job.useLog = job.tmmNormalize
+ job.countType =
+ if (expMeasure.toString.startsWith("Cufflinks")) {
+ if (isCuffIsoform) Option("CufflinksIsoform")
+ else Option("CufflinksGene")
+ } else Option(expMeasure.toString)
+ job
+ }
+
/** Merged gene fragment count table */
private lazy val geneFragmentsCountJob =
makeMergeTableJob((s: Sample) => s.geneFragmentsCount, ".fragments_per_gene", List(1), 2, fallback = "0")
- private lazy val geneFragmentsCountHeatmapJob = (geneFragmentsCountJob.isDefined && samples.size > 2)
- .option {
- val job = new PlotHeatmap(qscript)
- job.input = geneFragmentsCountJob.get.output
- job.output = new File(outputDir, "heatmap_fragments_per_gene.png")
- job.tmmNormalize = true
- job.useLog = true
- job.countType = Option("FragmentsPerGene")
- job
- }
+ private lazy val geneFragmentsCountHeatmapJob =
+ makeHeatmapJob(geneFragmentsCountJob, "fragments_per_gene", FragmentsPerGene)
/** Merged exon fragment count table */
- private def exonFragmentsCountJob =
+ private lazy val exonFragmentsCountJob =
makeMergeTableJob((s: Sample) => s.exonFragmentsCount, ".fragments_per_exon", List(1), 2, fallback = "0")
+ private lazy val exonFragmentsCountHeatmapJob =
+ makeHeatmapJob(exonFragmentsCountJob, "fragments_per_exon", FragmentsPerExon)
+
/** Merged gene base count table */
- private def geneBasesCountJob =
+ private lazy val geneBasesCountJob =
makeMergeTableJob((s: Sample) => s.geneBasesCount, ".bases_per_gene", List(1), 2, fallback = "0")
+ private lazy val geneBasesCountHeatmapJob =
+ makeHeatmapJob(geneBasesCountJob, "bases_per_gene", BasesPerGene)
+
/** Merged exon base count table */
- private def exonBasesCountJob =
+ private lazy val exonBasesCountJob =
makeMergeTableJob((s: Sample) => s.exonBasesCount, ".bases_per_exon", List(1), 2, fallback = "0")
+ private lazy val exonBasesCountHeatmapJob =
+ makeHeatmapJob(exonBasesCountJob, "bases_per_exon", BasesPerExon)
+
/** Merged gene FPKM table for Cufflinks, strict mode */
- private def geneFpkmCufflinksStrictJob =
- makeMergeTableJob((s: Sample) => s.geneFpkmCufflinksStrict, ".genes_fpkm_cufflinks_strict", List(1, 7), 10)
+ private lazy val geneFpkmCufflinksStrictJob =
+ makeMergeTableJob((s: Sample) => s.geneFpkmCufflinksStrict, ".genes_fpkm_cufflinks_strict", List(1, 7), 10, fallback = "0.0")
+
+ private lazy val geneFpkmCufflinksStrictHeatmapJob =
+ makeHeatmapJob(geneFpkmCufflinksStrictJob, "genes_fpkm_cufflinks_strict", CufflinksStrict)
/** Merged exon FPKM table for Cufflinks, strict mode */
- private def isoFpkmCufflinksStrictJob =
- makeMergeTableJob((s: Sample) => s.isoformFpkmCufflinksStrict, ".isoforms_fpkm_cufflinks_strict", List(1, 7), 10)
+ private lazy val isoFpkmCufflinksStrictJob =
+ makeMergeTableJob((s: Sample) => s.isoformFpkmCufflinksStrict, ".isoforms_fpkm_cufflinks_strict", List(1, 7), 10, fallback = "0.0")
+
+ private lazy val isoFpkmCufflinksStrictHeatmapJob =
+ makeHeatmapJob(isoFpkmCufflinksStrictJob, "isoforms_fpkm_cufflinks_strict", CufflinksStrict, true)
/** Merged gene FPKM table for Cufflinks, guided mode */
- private def geneFpkmCufflinksGuidedJob =
- makeMergeTableJob((s: Sample) => s.geneFpkmCufflinksGuided, ".genes_fpkm_cufflinks_guided", List(1, 7), 10)
+ private lazy val geneFpkmCufflinksGuidedJob =
+ makeMergeTableJob((s: Sample) => s.geneFpkmCufflinksGuided, ".genes_fpkm_cufflinks_guided", List(1, 7), 10, fallback = "0.0")
+
+ private lazy val geneFpkmCufflinksGuidedHeatmapJob =
+ makeHeatmapJob(geneFpkmCufflinksGuidedJob, "genes_fpkm_cufflinks_guided", CufflinksGuided)
/** Merged isoforms FPKM table for Cufflinks, guided mode */
- private def isoFpkmCufflinksGuidedJob =
- makeMergeTableJob((s: Sample) => s.isoformFpkmCufflinksGuided, ".isoforms_fpkm_cufflinks_guided", List(1, 7), 10)
+ private lazy val isoFpkmCufflinksGuidedJob =
+ makeMergeTableJob((s: Sample) => s.isoformFpkmCufflinksGuided, ".isoforms_fpkm_cufflinks_guided", List(1, 7), 10, fallback = "0.0")
+
+ private lazy val isoFpkmCufflinksGuidedHeatmapJob =
+ makeHeatmapJob(isoFpkmCufflinksGuidedJob, "isoforms_fpkm_cufflinks_guided", CufflinksGuided, true)
/** Merged gene FPKM table for Cufflinks, blind mode */
- private def geneFpkmCufflinksBlindJob =
- makeMergeTableJob((s: Sample) => s.geneFpkmCufflinksBlind, ".genes_fpkm_cufflinks_blind", List(1, 7), 10)
+ private lazy val geneFpkmCufflinksBlindJob =
+ makeMergeTableJob((s: Sample) => s.geneFpkmCufflinksBlind, ".genes_fpkm_cufflinks_blind", List(1, 7), 10, fallback = "0.0")
+
+ private lazy val geneFpkmCufflinksBlindHeatmapJob =
+ makeHeatmapJob(geneFpkmCufflinksBlindJob, "genes_fpkm_cufflinks_blind", CufflinksBlind)
/** Merged isoforms FPKM table for Cufflinks, blind mode */
- private def isoFpkmCufflinksBlindJob =
- makeMergeTableJob((s: Sample) => s.isoformFpkmCufflinksBlind, ".isoforms_fpkm_cufflinks_blind", List(1, 7), 10)
+ private lazy val isoFpkmCufflinksBlindJob =
+ makeMergeTableJob((s: Sample) => s.isoformFpkmCufflinksBlind, ".isoforms_fpkm_cufflinks_blind", List(1, 7), 10, fallback = "0.0")
+
+ private lazy val isoFpkmCufflinksBlindHeatmapJob =
+ makeHeatmapJob(isoFpkmCufflinksBlindJob, "isoforms_fpkm_cufflinks_blind", CufflinksBlind, true)
private lazy val mergedTables: Map[String, Option[MergeTables]] = Map(
"gene_fragments_count" -> geneFragmentsCountJob,
@@ -173,7 +212,16 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
)
private lazy val heatmapJobs: Map[String, Option[PlotHeatmap]] = Map(
- "gene_fragments_count_heatmap" -> geneFragmentsCountHeatmapJob
+ "gene_fragments_count_heatmap" -> geneFragmentsCountHeatmapJob,
+ "exon_fragments_count_heatmap" -> exonFragmentsCountHeatmapJob,
+ "gene_bases_count_heatmap" -> geneBasesCountHeatmapJob,
+ "exon_bases_count_heatmap" -> exonBasesCountHeatmapJob,
+ "gene_fpkm_cufflinks_strict_heatmap" -> geneFpkmCufflinksStrictHeatmapJob,
+ "isoform_fpkm_cufflinks_strict_heatmap" -> isoFpkmCufflinksStrictHeatmapJob,
+ "gene_fpkm_cufflinks_guided_heatmap" -> geneFpkmCufflinksGuidedHeatmapJob,
+ "isoform_fpkm_cufflinks_guided_heatmap" -> isoFpkmCufflinksGuidedHeatmapJob,
+ "gene_fpkm_cufflinks_blind_heatmap" -> geneFpkmCufflinksBlindHeatmapJob,
+ "isoform_fpkm_cufflinks_blind_heatmap" -> isoFpkmCufflinksBlindHeatmapJob
)
/** Output summary file */
--
GitLab