Howto render a tree with attributes in python toolkit ete?

Question

[whooli]

I'm using ete toolkit to get a phylogenetic tree for a list of ncbi taxids:

from ete2 import NCBITaxa
ncbi = NCBITaxa()
tree = ncbi.get_topology([9606, 9598, 10090, 7707, 8782])
print tree.get_ascii(attributes=["sci_name", "rank"])

Printing it with ascii chars works, but how to render this tree including the attributes (sci_name, rank) to an image?

tree.render("tree.pdf")

There seems to be no 'attribute' in this function.

Answer 1

[jhc]

tree.render() is a general purpose method. As node attributes are completely arbitrary, you need to specify what should be drawn and where... Check the docs regarding the drawing system: https://pythonhosted.org/ete2/tutorial/tutorial_drawing.html

For your example, something like this should work:

from ete2 import NCBITaxa, AttrFace, TreeStyle
ncbi = NCBITaxa()
tree = ncbi.get_topology([9606, 9598, 10090, 7707, 8782])

# custom layout: adds "rank" on top of branches, and sci_name as tip names
def my_layout(node):
    if getattr(node, "rank", None):
        rank_face = AttrFace("rank", fsize=7, fgcolor="indianred")
        node.add_face(rank_face, column=0, position="branch-top")
    if node.is_leaf():
        sciname_face = AttrFace("sci_name", fsize=9, fgcolor="steelblue")
        node.add_face(sciname_face, column=0, position="branch-right")
ts = TreeStyle()
ts.layout_fn = my_layout
ts.show_leaf_name = False
tree.render("tree.png", tree_style=ts)

[whooli]

thank you, that's what I was looking for!

Answer 2

[AndreiR]

Have you tried:

from ete2 import NCBITaxa
ncbi = NCBITaxa()
tree = ncbi.get_topology([9606, 9598, 10090, 7707, 8782]) 

ncbi.annotate_tree(tree,taxid_attr='name')

from https://pythonhosted.org/ete2/reference/reference_ncbi.html

[jhc]

What annotate_tree does is to read a bare tree and add the rank, sci_name, taxid attrs automatically (by parsing taxids from tip names, for instance). It is very useful to annotate your own trees, but the tree objects returned by ncbi.get_topology() are already annotated.

[AndreiR]

Nice! Haven't used get_topology. Thanks.