From fccd5517a0ea77931cb056001ec80f9d19849ae6 Mon Sep 17 00:00:00 2001
From: corin <corin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 26 May 2011 20:13:59 +0000
Subject: [PATCH] Generates post run QC plots with by sample metrics

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5884 348d0f76-0448-11de-a6fe-93d51630548a
---
 R/DataProcessingReport/newpostqc.r | 41 ++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)
 create mode 100644 R/DataProcessingReport/newpostqc.r

diff --git a/R/DataProcessingReport/newpostqc.r b/R/DataProcessingReport/newpostqc.r
new file mode 100644
index 000000000..6544aa06f
--- /dev/null
+++ b/R/DataProcessingReport/newpostqc.r
@@ -0,0 +1,41 @@
+source("/humgen/gsa-pipeline/.repository/R/DataProcessingReport/qcplots.r")
+suppressMessages(library(gplots));
+def.par <- par(no.readonly = TRUE)
+
+
+cmdargs = gsa.getargs(
+    list(
+        tsv = list(value=NA, doc="pipeline tsv file"),
+        evalroot = list(value=NA, doc="VariantEval file base (everything before the .eval)"),
+        reportout = list(value=NA, doc="Output path for report PDF")#,
+    ),
+    doc="Creates a variant report"
+);
+
+read.delim(cmdargs$tsv, header=FALSE)->settable
+
+squids<-unique(settable[,1])
+
+
+gsa.read.gatkreport(paste(cmdargs$evalroot, ".eval", sep=""))->basiceval 
+gsa.read.gatkreport(paste(cmdargs$evalroot, ".extraSA.eval", sep=""))->SAeval 
+print("Evals read")
+
+pdf(file= cmdargs$reportout, width=22, height=17, pagecentre=TRUE, pointsize=24) 
+    print("PDF created...")
+
+
+path="."
+weirdos<-which(SAeval$TiTvVariantEvaluator$Sample %in% SAeval$TiTvVariantEvaluator$Sample[which(SAeval$TiTvVariantEvaluator$tiTvRatio <2)])
+
+novelAC(SAeval)
+knownAC(SAeval)
+AllAC(SAeval)
+layout(matrix(c(6,1, 2,3, 4, 5), nrow=6), heights=c(1, 1, 1, 1, 1,1)) 
+textplot("Sample Novel TiTv ranges should be above 2, as they are in previous datasets. \nSamples with lower TiTv data are flagged in subsequent plots with hot pink labels, and listed below:")
+textplot(paste(unique(SAeval$TiTvVariantEvaluator$Sample[weirdos]), collapse=", "), halign="left")
+textplot("Problem Samples frequently have unusually high or low numbers of variants.")
+textplot("Samples with unusually high numbers of novel variants may be from different populations, and, as such, should have higher heterozygosity. \nIf this is not the case, there may be problems with the samples.")
+textplot("Unusually high numbers of variants with low allele counts may indicate variants generated from problematic samples.")
+textplot("Notes for interpreting QC data:")
+dev.off()