# HG changeset patch
# User boris
# Date 1374270298 14400
# Node ID dd39849c2ff1fe71750d42175e87de9ca81d08c8
# Parent  369f0b641498bc8e55d99581c315693d6a36dbd1
plot now highlights minor allele sequences in tree

diff -r 369f0b641498 -r dd39849c2ff1 phylorelatives.py
--- a/phylorelatives.py	Tue Jun 25 00:41:54 2013 -0400
+++ b/phylorelatives.py	Fri Jul 19 17:44:58 2013 -0400
@@ -97,45 +97,27 @@
     return ascii_tree
 
 
-def ape_plot_tree(outfile, tree1, tree2=None, root=False):
+def ape_plot_tree(outfile, tree1, root=False):
     """Plot tree to png file"""
     ape = importr('ape')
     graphics  = importr('graphics')
     grdevices = importr('grDevices')
-    if tree2 is None:
-        grdevices.png(file=outfile, width=1024, height=768)
-        if root:
-            ape.plot_phylo(ape.root(tree1,root),use_edge_length=0,
-                          show_node_label=1,edge_width=2, font=2,
-                          cex=1,underscore=0, no_margin=1)
-        else:
-            ape.plot_phylo(tree1,use_edge_length=0,
-                          show_node_label=1,edge_width=2, font=2,
-                          cex=1,underscore=0, no_margin=1)
-        #graphics.title(main='Neighbor Joining')
-        grdevices.dev_off()
-    elif tree2 is not None:
-        grdevices.png(file=outfile, width=1024, height=768)
-        graphics.par(mfcol=array.array('i',[1,2]))
-        if root:
-            ape.plot_phylo(ape.root(tree1,root),use_edge_length=0,
-                          show_node_label=1,edge_width=2, font=2,
-                          cex=1,underscore=0, no_margin=1)
-        else:
-            ape.plot_phylo(tree1,use_edge_length=0,
-                          show_node_label=1,edge_width=2, font=2,
-                          cex=1,underscore=0, no_margin=1)
-        graphics.title(main='Neighbor Joining', cex=1.5, font=2)
-        if root:
-            ape.plot_phylo(ape.root(tree2,root),use_edge_length=0,
-                          show_node_label=1,edge_width=2, font=2,
-                          cex=1,underscore=0, no_margin=1)
-        else:
-            ape.plot_phylo(tree2,use_edge_length=0,
-                          show_node_label=1,edge_width=2, font=2,
-                          cex=1,underscore=0, no_margin=1)
-        graphics.title(main='Maximum Parsimony',cex=1.5, font=2)
-        grdevices.dev_off()
+    grdevices.png(file=outfile, width=1024, height=768)
+    if root:
+        tree = ape.root(tree1,root)
+        labels = list(tree.rx("tip.label")[0])
+        colors = robjects.StrVector(["red" if tip.endswith("_minor") else "black" for tip in labels])
+        ape.plot_phylo(tree,tip_color=colors,use_edge_length=0,
+                      show_node_label=1,edge_width=2, font=2,
+                      cex=1,underscore=0, no_margin=1)
+    else:
+        tree = tree1
+        labels = list(tree.rx("tip.label")[0])
+        colors = robjects.StrVector(["red" if tip.endswith("_minor") else "black" for tip in labels])
+        ape.plot_phylo(tree,tip_color=colors,use_edge_length=0,
+                      show_node_label=1,edge_width=2, font=2,
+                      cex=1,underscore=0, no_margin=1)
+    #graphics.title(main='Neighbor Joining')
     return