--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/alignvis.py	Sat Mar 10 07:59:27 2012 -0500
@@ -0,0 +1,76 @@
+import sys,os
+
+infile = sys.argv[1]
+outfile = sys.argv[2]
+uselog = sys.argv[3]
+subset = sys.argv[4]
+reorder = sys.argv[5]
+color = sys.argv[6]
+scale = sys.argv[7] # rescale each row
+rscript = open('tmp.r','w')
+
+rscript.write("x <- read.table('"+infile+"')\n")
+rscript.write("nfeat <- nrow(x) \n")
+rscript.write("nbin <- ncol(x) - 2\n")
+rscript.write("totalcov <- x[,2]\n")
+rscript.write("x <- x[,3:ncol(x)]\n")
+
+if subset =='subset':
+    rscript.write("if (nfeat*nbin > 100000) {\n")
+    rscript.write("  nfeat2 <- as.integer(100000/nbin)\n")
+    rscript.write("  subind <- sample(seq(nfeat),nfeat2)\n")
+    rscript.write("  x <- x[subind,]\n")
+    rscript.write("  totalcov <- totalcov[subind]\n")
+    rscript.write("}\n")
+
+rscript.write("pdf('"+outfile+"')\n")
+
+if uselog == 'uselog':
+    rscript.write("x <- -(log(1+as.matrix(x,nc=ncol(x)-2)))\n")
+else:
+    rscript.write("x <- -as.matrix(x,nc=ncol(x)-2)\n")
+if scale == 'scale':
+    rscript.write("x <- scale(x)\n")
+if reorder == 'average':
+    rscript.write("hc <- hclust(dist(x),method= 'average')\n")
+    rscript.write("x <- x[hc$order,]\n")
+elif reorder == 'centroid':
+    rscript.write("hc <- hclust(dist(x),method= 'centroid')\n")
+    rscript.write("x <- x[hc$order,]\n")
+elif reorder == 'complete':
+    rscript.write("hc <- hclust(dist(x),method= 'complete')\n")
+    rscript.write("x <- x[hc$order,]\n")
+elif reorder == 'single':
+    rscript.write("hc <- hclust(dist(x),method= 'single')\n")
+    rscript.write("x <- x[hc$order,]\n")
+elif reorder == 'median':
+    rscript.write("hc <- hclust(dist(x),method= 'median')\n")
+    rscript.write("x <- x[hc$order,]\n")    
+elif reorder == 'sort_by_total':
+    rscript.write("srt <- sort(totalcov,index.return=T)\n")
+    rscript.write("x <- x[srt$ix,]\n")
+elif reorder == 'sort_by_center':
+    rscript.write("srt <- sort(x[,as.integer(nbin/2)],index.return=T)\n")
+    rscript.write("x <- x[srt$ix,]\n")
+if color == 'heat':
+    rscript.write("colormap = heat.colors(1000)\n")
+elif color == 'topo':
+    rscript.write("colormap = topo.colors(1000)\n")
+elif color == 'rainbow':
+    rscript.write("colormap = rainbow(1000)\n")
+elif color == 'terrain':
+    rscript.write("colormap = terrain.colors(1000)\n")
+else:
+    rscript.write("colormap = gray.colors(1000)\n")
+
+#rscript.write("qt <- quantile(as.vector(x),probs=c(0.1,0.9))\n")
+#rscript.write("breaks <- c(min(as.vector(x)),seq(qt[1],qt[2],length.out=99),max(as.vector(x)))\n")
+#rscript.write("image(t(x),col=colormap,breaks=breaks,axes=F)\n")
+rscript.write("image(t(x),col=colormap,axes=F)\n")
+rscript.write("dev.off()\n")
+
+rscript.close()
+
+os.system("R --slave < tmp.r")
+os.system("rm tmp.r")
+