New plotter for phylogenetic trees: customization

Continuing with a tree-plotter in Python. Previous posts here, here, and here. These examples depend on PyCogent and matplotlib.

I've got a somewhat bigger tree here, using sequences from a project we're working on. I used clustal and R to make a neighbor-joining tree. As you can see in the code, there is a lot of flexibility in terms of customized colors, etc.

code listing:

import tree_utils as TU import tree_plotter as TP fn = 'veillonella.tree.txt' D = TU.make_tree_dict(fn=fn) tr = D['meta']['tree'] attr = TP.get_default_attr() attr['e_node_dot_size'] = 35 attr['figure_type'] = 'png' attr['e_node_label_size'] = 10 attr['e_node_bar_color'] = 'k' attr['using_alternate_names'] = True e_node_names = D['meta']['e_node_names'] #L = [e.replace('_',' ') for e in e_node_names] L = [e.split('_')[-1] for e in e_node_names] # lose the version numbers on Genbank seqs L = [e.split('.')[0] for e in e_node_names] alt_name_dict = dict(zip(e_node_names,L)) attr['alternate_name_dict'] = alt_name_dict attr['using_e_node_specific_colors'] = True def f(name): if 'DB' in name: return 'b' return 'r' L = [f(e) for e in e_node_names] node_label_color_dict = dict(zip(e_node_names,L)) attr['node_label_color_dict'] = node_label_color_dict def f(name): if 'DB' in name: return 'b' return 'r' L = [f(e) for e in e_node_names] dot_color_dict = dict(zip(e_node_names,L)) attr['dot_color_dict'] = dot_color_dict TP.plot(D,attr=attr) ''' Rcode: library(ape) setwd('Desktop') dna = read.dna('veillonella.fasta',format='fasta') tree = nj(dist.dna(dna)) plot(tree,cex=1) axisPhylo() write.tree(tree,'veillonella.tree.txt') '''