minor fixes

Author: Mark Fiers

hagfish_blockcompplot

@@ -25,6 +25,10 @@ parser.remove_option('-Y')
 parser.remove_option('--ymax')
 parser.remove_option('-Q')
 
+
+parser.add_option('-L', dest='library2', action='append',
+                  help='Library to compare to')
+
 options, args = parser.parse_args()
 
 options.ymax = 2
@@ -36,21 +40,10 @@ l.info("starting %s" % sys.argv[0])
 
 seqId = args[0]
 
-indir1 = args[1]
-indir2 = args[2]
-
-infile1 = os.path.join(
-    indir1, 'combined', 
-    '%s.combined.coverage.npz' % seqId)
-l.info("input file 1: %s" % infile1)
-infile2 = os.path.join(
-    indir2, 'combined', 
-    '%s.combined.coverage.npz' % seqId)
-l.info("input file 2: %s" % infile2)
 
 #load the coverage plots
-data = hagfishData(options, args, inputFile = infile1)
-data2 = hagfishData(options, args, inputFile = infile2)
+data = hagfishData(options, args)
+data2 = hagfishData(options, args, libraries=options.library2)
 
 #prepare the plot
 plot = hagfishPlot(options, data, data2=data2)

hagfish_blockcompplot2

@@ -43,6 +43,9 @@ seqId = args[0]
 data = hagfishData(options, args)
 data2 = hagfishData(options, args, libraries=options.library2)
 
+title1 = "_".join(options.library)
+title2 = "_".join(options.library2)
+
 #prepare the plot
 plot = hagfishPlot(options, data, data2=data2, tag='blockcomp')
 
@@ -78,6 +81,22 @@ class plotter(hagfishPlotBand):
             extent=[0 , len(self.locx),
                     self.bandBottom + spacer, self.bandTop]
             )
+
+
+        if self.__dict__.has_key('nns'):
+            self.l.info("plotting N band")
+            self.l.info("maxY %s" % self.plot.maxY)
+            self.l.info("max min nns %s %s " % (np.max(self.nns), np.min(self.nns)))
+            self.l.info("bandbot, bandtop %s %s " % (self.bandBottom, self.bandTop))
+
+
+            self.ax.fill_between(
+                self.locx,
+                yc + (self.plot.maxY * self.nns * 0.25),
+                yc - (self.plot.maxY * self.nns * 0.25),
+                linewidth=0, zorder=220,
+                color=COLLIGHTYELLOW)
+
 
     def setYticks2(self):
         pass
@@ -94,6 +113,6 @@ cb.set_ticklabels(['resembles "%s"' % ", ".join(options.library) ,
                    'resembles "%s"' % ", ".join(options.library2)])
 #                    0, -1],
 #3             aspect=80,
-plot.save()
+plot.save(libname='%s.%s' % (title1,title2))
 
 

hagfish_compplot2

@@ -173,22 +173,22 @@ class plotter(hagfishPlotBand):
 
 
     def setYticks2(self):
-        self.plot.yTicks2.append(self.yCorrection - self.data.medianH)
+        self.plot.yTicks2.append(self.yCorrection - self.data.median)
         self.plot.yTicks2.append(self.yCorrection)
-        self.plot.yTicks2.append(self.yCorrection + self.data.medianH)
-        self.plot.yTickLabels2.append("%s" % -self.data.medianH)
+        self.plot.yTicks2.append(self.yCorrection + self.data.median)
+        self.plot.yTickLabels2.append("%s" % -self.data.median)
         self.plot.yTickLabels2.append("0")
-        self.plot.yTickLabels2.append("%s" % self.data.medianH)
+        self.plot.yTickLabels2.append("%s" % self.data.median)
         self.ax.axhline(
-            self.yCorrection - self.data.medianH,
+            self.yCorrection - self.data.median,
             alpha=0.3,
             color='black')
         self.ax.axhline(
-            self.yCorrection + self.data.medianH,
+            self.yCorrection + self.data.median,
             alpha=0.3,
             color='black')
 
 plot.plotBands(plotter)
-plot.save(tag='%s.%s.comp' % (title1,title2))
+plot.save(tag='%s.%s.compplot2' % (title1,title2))