Python for Bioinformatics: PyCogent 13: Tree with colored edges

Thursday, December 10, 2009

PyCogent 13: Tree with colored edges

I'm exploring PyCogent (docs, download page)---first post here.

Continuing from the last post, we use PyCogent to plot the tree. By looking at the source code, I figured out how to color the edges, but I haven't seen how to color the tip labels. It would also be useful to be able to edit the labels.

from cogent import LoadTree
from cogent.draw import dendrogram

fn = 'temp.tree'
t = LoadTree(fn)

def f(node):
    L = ['DQ450530','AJ278451','AF411020']
    if node.isTip():
        name = node.getTipNames()[0]
        for e in L:
            if e in name:  return 'blue'
        return 'red'
    return 'black'

height, width = 500,500
np = dendrogram.ContemporaneousDendrogram(t)
np.drawToPDF('temp.pdf',
             width,
             height,
             font_size=14,
             edge_color_callback=f)