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Slightly nicer plotting; not yet complete 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3961 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2010-08-06 20:01:31 +00:00
parent f275041b1c
commit bb5dfd7e5e
1 changed files with 20 additions and 10 deletions
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30
R/VariantRecalibratorReport/VariantRecalibratorReport.R
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@ -14,10 +14,11 @@ vcfTable = args[3];
if (is.na(vcfTable)) { vcfTable = "/home/radon01/kiran/scr1/projects/DataProcessingPaper/scratch/MarkBustedWEx.table"; } if (is.na(vcfTable)) { vcfTable = "/home/radon01/kiran/scr1/projects/DataProcessingPaper/scratch/MarkBustedWEx.table"; }
lociFile = args[4]; lociFile = args[4];
if (is.na(lociFile)) { lociFile = "/home/radon01/kiran/scr1/projects/DataProcessingPaper/scratch/MarkBustedWEx.loci"; } if (is.na(lociFile) | lociFile == "NA" ) { lociFile = "/home/radon01/kiran/scr1/projects/DataProcessingPaper/scratch/MarkBustedWEx.loci"; }
maxVariants = args[5]; maxVariants = args[5];
if (is.na(maxVariants)) { maxVariants = -1; } if (is.na(maxVariants)) { maxVariants = -1; }
maxVariants = as.integer(maxVariants)
getAnnIndex <- function(d, ann) { getAnnIndex <- function(d, ann) {
index = -1; index = -1;
@ -123,8 +124,12 @@ plotClusters <- function(d.known, d.novel, d.loci, c, ann1, ann2, filename, maxV
mult2 = c[[1]]$conversions[[cindex2]]$multiplier; mult2 = c[[1]]$conversions[[cindex2]]$multiplier;
off2 = c[[1]]$conversions[[cindex2]]$offset; off2 = c[[1]]$conversions[[cindex2]]$offset;
xlims = c(min((d.novel[,index1] - off1)/mult1), 1.2*max((d.novel[,index1] - off1)/mult1)); xvalsForLims = c(-5, 5)
ylims = c(min((d.novel[,index2] - off2)/mult2), max((d.novel[,index2] - off2)/mult2)); yvalsForLims = c(-5, 5)
#xvalsForLims = (d.known[,index1] - off1)/mult1
#yvalsForLims = (d.known[,index2] - off2)/mult2
xlims = c(min(xvalsForLims), 1.2*max(xvalsForLims));
ylims = c(min(yvalsForLims), max(yvalsForLims));
clusterColors = c("#A62103", "#F27405", "#F29F05", "#F2B705", "#F2CB05"); clusterColors = c("#A62103", "#F27405", "#F29F05", "#F2B705", "#F2CB05");
@ -133,10 +138,14 @@ plotClusters <- function(d.known, d.novel, d.loci, c, ann1, ann2, filename, maxV
par(mar=c(5, 6, 2, 5)); par(mar=c(5, 6, 2, 5));
plot(0, 0, type="n", xaxt="n", yaxt="n", xlim=xlims, ylim=ylims, xlab=ann1, ylab=ann2, bty="n"); plot(0, 0, type="n", xaxt="n", yaxt="n", xlim=xlims, ylim=ylims, xlab=ann1, ylab=ann2, bty="n");
mv.known = ifelse(maxVariants == -1, nrow(d.known), maxVariants); mv.known = if (maxVariants == -1 | maxVariants >= nrow(d.known)) { seq(1, nrow(d.known)) } else { as.integer(runif(maxVariants, 1, nrow(d.known)+1))}
mv.novel = ifelse(maxVariants == -1, nrow(d.novel), maxVariants); mv.novel = if (maxVariants == -1 | maxVariants >= nrow(d.novel)) { 1:nrow(d.novel) } else { as.integer(runif(maxVariants, 1, nrow(d.novel)+1)) }
points(((d.known[,index1] - off1)/mult1)[1:mv.known], ((d.known[,index2] - off2)/mult2)[1:mv.known], pch=19, cex=0.4, col="blue");
points(((d.novel[,index1] - off1)/mult1)[1:mv.novel], ((d.novel[,index2] - off2)/mult2)[1:mv.novel], pch=19, cex=0.4, col="red"); print(dim(mv.known))
print(maxVariants)
points(((d.known[,index1] - off1)/mult1)[mv.known], ((d.known[,index2] - off2)/mult2)[mv.known], pch=19, cex=0.3, col="#0000FF33");
points(((d.novel[,index1] - off1)/mult1)[mv.novel], ((d.novel[,index2] - off2)/mult2)[mv.novel], pch=19, cex=0.3, col="#FF000033");
for (clusterIndex in c(1:length(c))) { for (clusterIndex in c(1:length(c))) {
mu = c(c[[clusterIndex]]$means[cindex1], c[[clusterIndex]]$means[cindex2]); mu = c(c[[clusterIndex]]$means[cindex1], c[[clusterIndex]]$means[cindex2]);
@ -161,7 +170,7 @@ plotClusters <- function(d.known, d.novel, d.loci, c, ann1, ann2, filename, maxV
else if (weight > 0.60 && weight <= 0.80) { color = clusterColors[4]; } else if (weight > 0.60 && weight <= 0.80) { color = clusterColors[4]; }
else if (weight > 0.80) { color = clusterColors[5]; } else if (weight > 0.80) { color = clusterColors[5]; }
lineweight = ifelse(weight > 0.50, 2, 1); lineweight = ifelse(weight > 0.50, 4, 3);
points(mu[1], mu[2], pch=21, col=color, cex=0.5); points(mu[1], mu[2], pch=21, col=color, cex=0.5);
points(ellipse(t(cov), centre=mu), type="l", lwd=lineweight, col=color); points(ellipse(t(cov), centre=mu), type="l", lwd=lineweight, col=color);
@ -208,14 +217,15 @@ plotClusters <- function(d.known, d.novel, d.loci, c, ann1, ann2, filename, maxV
dev.off(); dev.off();
} }
d = read.table(vcfTable, header=TRUE);
c = read.clusters(clusterFile);
l = c(); l = c();
if (!is.na(lociFile)) { if (!is.na(lociFile)) {
t = read.table(lociFile, header=TRUE); t = read.table(lociFile, header=TRUE);
l = t$POS; l = t$POS;
} }
d = read.table(vcfTable, header=TRUE);
c = read.clusters(clusterFile);
d.known = d[which(d$DB == 1),]; d.known = d[which(d$DB == 1),];
d.novel = d[which(d$DB == 0),]; d.novel = d[which(d$DB == 0),];
d.loci = NA; d.loci = NA;