Mercurial > repos > boris > phylorelatives

changeset 40:dd39849c2ff1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
plot now highlights minor allele sequences in tree
author boris
date Fri, 19 Jul 2013 17:44:58 -0400
parents 369f0b641498
children 9453ba52f46b
files phylorelatives.py
diffstat 1 files changed, 17 insertions(+), 35 deletions(-) [+]
line wrap: on
line diff
--- 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