changeset 2:57c5ea9c3c5c draft

Uploaded

--- a/hetbox.py	Thu Jun 13 15:10:09 2013 -0400
+++ b/hetbox.py	Fri Jun 21 16:05:46 2013 -0400
@@ -8,6 +8,7 @@
 
 import os
 import sys
+import array
 import numpy
 from rpy2.robjects import Formula
 from rpy2.robjects.packages import importr
@@ -49,6 +50,7 @@
       +"line.\nAdding an artificial header..")
     add_header = True
 
+r = robjects.r
 base = importr('base')
 utils = importr('utils')
 stats = importr('stats')
@@ -86,24 +88,31 @@
 # The "environment" in .getenvironment() is the entire R workspace in which the
 # Formula object exists. The R workspace meaning all the defined variables.
 # Here, the .getenvironment() method is being used to set some variables in the
+# R workspace
 
-# R workspace
 formula.getenvironment()['minor_freq'] = minor_freq
 formula.getenvironment()['samples']    = samples
 
+
+r.par(oma=array.array('i', [0,0,0,0]))
+r.par(mar=array.array('i', [10,4,4,2]))
+ylimit = array.array('i',[-5,50])
+
 # create boxplot - fill kwargs1 with the options for the boxplot function
 kwargs1 = {'ylab':"Minor allele frequency (%)", 'col':"gray", 'xaxt':"n",
            'outpch':"*",'main':"Distribution of minor allele frequencies",
            'cex.lab':"1.5"}
-p = graphics.boxplot(formula, **kwargs1)
-table  = base.table(DATA.rx2('SAMPLE'))
-graphics.text(0.5, 1, 'N:', font=2)
+p = graphics.boxplot(formula, axes=0,ylim=ylimit, lty=1,**kwargs1)
+
+table = base.table(DATA.rx2('SAMPLE'))
+#graphics.text(-1, 1, 'N:', font=2)
 for i in range(1, base.length(table)[0]+1, 1):
-    graphics.text(i, 1, table[i-1], font=2)
+    graphics.text(i, -1, table[i-1], font=2)
 
 graphlabels = base.names(table)
-kwargs3 = {'pos':"0", 'las':"2", 'cex.axis':"1"}
-graphics.axis(1, at=range(1, len(graphlabels)+1, 1), labels=graphlabels, **kwargs3)
+kwargs3 = {'pos':"-2", 'las':"2", 'cex.axis':"1"}
+graphics.axis(1, at=range(1, len(graphlabels)+1, 1),labels=graphlabels, **kwargs3)
+graphics.axis(2,at=(range(0,60,10)),pos=0,font=2)
 grdevices.dev_off()
 
 if not report: