O.rka O.rka - 2 months ago 11
Python Question

How to color leaves on `ete3` Tree? (Python 3)

I just started using

ete3
and it is awesome.

How can I color the leaves of an
ete3
Tree object using a color dictionary?
I made
"c":None
because I don't want the of
c
to show up.

I want to have better control of the tree render but I can't figure out exactly how to do it.

I saw that there are
NodeStyle
objects
but I think this is for the actual nodes. It looks like this
TextFace
object
is what I need but I don't know how to use it. All the examples are adding labels.

# Build Tree
tree = ete3.Tree( "((a,b),c);" )
# Leaf mapping
D_leaf_color = {"a":"r", "b":"g","c":None}
# Set up style for circular tree
ts = ete3.TreeStyle()
ts.mode = "c"
# Draw Tree
tree.render("tree_test.png", dpi=300, w=500, tree_style=ts)


enter image description here

I looked at this question but it was pretty confusing:
How to color tree nodes with fixed set of colors?

jhc jhc
Answer

I would do it like this:

from ete3 import Tree, TextFace, TreeStyle

# Build Tree
tree = Tree( "((a,b),c);" )
# Leaf mapping
D_leaf_color = {"a":"red", "b":"green"}
for node in tree.traverse():
    # Hide node circles
    node.img_style['size'] = 0
    if node.is_leaf():
        color = D_leaf_color.get(node.name, None)
        if color:
            name_face = TextFace(node.name, fgcolor=color, fsize=10)
            node.add_face(name_face, column=0, position='branch-right')
# Set up style for circular tree
ts = TreeStyle()
ts.mode = "c"
ts.scale = 10
# Disable the default tip names config
ts.show_leaf_name = False
ts.show_scale = False
# Draw Tree
tree.render("tree_test.png", dpi=300, w=500, tree_style=ts)

enter image description here

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