ETE2：向节点添加图像

Question

I have been trying to add different images to nodes in a phylogenetic tree using the ete2 software in Python, but have no success.

from ete2 import Tree, TreeStyle, NodeStyle, TextFace, faces, add_face_to_node, AttrFace
ts.show_leaf_name = True
ts.show_branch_support = True

nw = """
(((Dre:0.008339,Dme:0.300613)1.000000:0.596401,
(Cfa:0.640858,Hsa:0.753230)1.000000:0.182035)1.000000:0.106234,
((Dre:0.271621,Cfa:0.046042)1.000000:0.953250,
(Hsa:0.061813,Mms:0.110769)1.000000:0.204419)1.000000:0.973467);
"""
t = Tree(nw)


img_path = "/home/leonard/Desktop/img_faces/"

humanFace = faces.ImgFace(img_path+"human.png")

mouseFace = faces.ImgFace(img_path+"mouse.png")


def my_layout(node):

 if name.startswith("Dre"):

  faces.add_face_to_node(humanface, node, column=1)

t.show(my_layout)

ts = TreeStyle()

t.render("img_faces.png", w=600, tree_style = ts)

These are error messages that I have been getting:

 File "abc1.py", line 34, in <module>
    t.show(my_layout)
  File "/usr/local/lib/python2.7/dist-packages/ete2-2.1rev544-py2.7.egg/ete2/coretype/tree.py", line 1283, in show
    drawer.show_tree(self, layout=layout, tree_style=tree_style)
  File "/usr/local/lib/python2.7/dist-packages/ete2-2.1rev544-py2.7.egg/ete2/treeview/drawer.py", line 84, in show_tree
    tree_item, n2i, n2f = render(t, img)
  File "/usr/local/lib/python2.7/dist-packages/ete2-2.1rev544-py2.7.egg/ete2/treeview/qt4_render.py", line 258, in render
    set_style(n, layout_fn)
  File "/usr/local/lib/python2.7/dist-packages/ete2-2.1rev544-py2.7.egg/ete2/treeview/qt4_render.py", line 746, in set_style
    layout_func(n)
  File "abc1.py", line 29, in my_layout
    if name.startswith("Dre"):
NameError: global name 'name' is not defined

Any help is much appreciated!

Answer 1

This is the solution from Jaime Huerta Cepas in google group, and I quote:

"There is a general Python programming error in your script ("name" variable does not exist). I guess that what you meant is "node.name.startswith()" instead of "name.startswith()""

It worked.

Answer 2

According to the documentation ( ete2 ) you need to create a faces ready to read the name attribute of nodes.

Try to add the following to your code:

#nameFace = faces.TextFace(open("text").readline().strip(), fsize=20, fgcolor="#009000")
nameFace = faces.AttrFace("name", fsize=20, fgcolor="#009000")