How to change the font orientation on node labels?

[Marko Manninen]

I asked this question jsut recently on stackoverflow.com. You might want to add ete-toolkit label there (if some users has enough points to create new labels) and follow related questions.

http://stackoverflow.com/questions/35551004/how-to-change-the-font-orientation-on-node-labels-with-ete-toolkit-python

I'd like to change the orientation of font faces on the output image that is produced by ETE Toolkit: http://etetoolkit.org For some reason rotation and orientation change does not affect to labels as seen on the picture below: Code to produce this example on the Jupiter notebook is following: from ete3 import Tree, TreeStyle def draw_ete(newick): t = Tree(newick) ts = TreeStyle() ts.scale = 5 ts.rotation = -90 ts.orientation = 1 return t.render("%%inline", tree_style=ts) newick = """((p, e, a, s, ((e, _), p, o), r, r, i, d, g, (e, _)), (h, o, t), ((，, ↵), (p, e, a, s, ((e, _), p, o), r, r, i, d, g, (e, _))), (c, (o, l, d)), ((，, ↵), (p, e, a, s, ((e, _), p, o), r, r, i, d, g, (e, _))), ((i, n), _, t, h, ((e, _), p, o), t, (，, ↵), n, (i, n), (e, _), d, a, y, s, _, (o, l, d), .), ↵, ↵, (s, o, m, (e, _), l, i, k, (e, _), i, t, _), (h, o, t), ((，, ↵), (s, o, m, (e, _), l, i, k, (e, _), i, t, _)), (c, (o, l, d)), ((，, ↵), (s, o, m, (e, _), l, i, k, (e, _), i, t, _)), ((i, n), _, t, h, ((e, _), p, o), t, (，, ↵), n, (i, n), (e, _), d, a, y, s, _, (o, l, d), .));""" draw_ete(newick) I would also like to know if it is possible to split the output to multiple rows instead of one line? Long sequences tend to take huge width space so it would be practical to get sequence split on several lines.

Third question is: how to remove |-----| {num} endin from the image?

Thanks in forehand!
-Marko

[Jaime Huerta Cepas]

Hi Marko, 

1) rotation is possible by using custom layouts and TextFaces. 

Check this example: https://github.com/etetoolkit/ete/blob/master/examples/treeview/face_rotation.py

which produces something similar to this image: http://etetoolkit.org/static/img/gallery/rotatedface400x400.png

2) split on several lines: I don't fully understand your questions. If asking about reducing the width of the final tree image, the only way would be to split de drawing in multiple render calls, one per node that you want to draw. 

For instance. To split one tree into two independent images, you could run: 

t.children[0].render("left_side.png")

and 

t.children[1].render("right_side.png")

3) You mean the branch scale at bottom?

You  can set TreeStyle.show_scale=False 

best, 

-jaime 

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[Marko Manninen]

Hi Jamie,

great timing!

1) I will try rotation with example you gave. I already tried rotation attribute but I have missed something...

2) If possible I'd like to get that rendered on a notebook. I suppose %%inline printer does not support this kind of multiple rendered images on a same cell behavior? Should I first save two independent images and then combine them as one with some image manipulation utility? I think you understood correctly what I'm looking for, but poorly could describe.

3) simple and working.

-Marko

[Jaime Huerta Cepas]

2) If possible I'd like to get that rendered on a notebook. I suppose %%inline printer does not support this kind of multiple rendered images on a same cell behavior? Should I first save two independent images and then combine them as one with some image manipulation utility? I think you understood correctly what I'm looking for, but poorly could describe.

It should work the same with %%inline. 

But yes, I am afraid you will need to concatenate all partial images vertically (you can try to automate it with i.e. imagemagick ...)   

 

[Marko Manninen]

Thanks for all help! I got it all working pretty well:

from ete3 import Tree, TreeStyle, NodeStyle, TextFace

from IPython.display import HTML

def tree_style(rotation):

    # define node/leaf modifier

    def rotate_labels(node):

        ns = NodeStyle()

        ns["size"] = 1

        if node.is_leaf():

            F = TextFace(node.name)

            F.rotation = rotation

            F.margin_right = F.margin_left = 2.0

            node.add_face(F, 0, position="aligned")

        node.img_style = ns

    

    # init tree style

    ts = TreeStyle()

    # scale of the figure

    ts.scale = 10

    # remove default labels

    ts.show_leaf_name = False

    # hide scale

    ts.show_scale = False

    # rotate 90 degress counterclockwise

    ts.rotation = rotation

    # orient tree from left to right

    ts.orientation = 1

    # rotate labels

    ts.layout_fn = rotate_labels

    return ts

def get_tree(newick_str):

    # init tree

    return Tree(newick_str)

def branches(newick_str, rotation = -90):

    # get tree instance

    t = get_tree(newick_str)

    # length of the tree

    l = len(t.children)

    # create inline display object from each tree branch

    return [t.children[i].render("%%inline", tree_style=tree_style(rotation)) for i in range(l)]

def main(newick_str):

    # iterate over all branches on a tree and base64 encode image data for the img tag

    imagesList = ''.join(['<div style="height:100px;float:left;"><img src="data:image/png;base64,%s" /></div>' 

                       % base64.b64encode(branch.data).decode() for branch in branches(newick_str)])

    # display on jupyter notebook cell

    return HTML(imagesList)

# init a newick string

newick_str = """((p, e, a, s, ((e, _), p, o), r, r, i, d, g, (e, _)), (h, o, t), ((，, ↵), (p, e, a, s, ((e, _), p, o), r, r, i, d, g, (e, _))), (c, (o, l, d)), ((，, ↵), (p, e, a, s, ((e, _), p, o), r, r, i, d, g, (e, _))), ((i, n), _, t, h, ((e, _), p, o), t, (，, ↵), n, (i, n), (e, _), d, a, y, s, _, (o, l, d), .), ↵, ↵, (s, o, m, (e, _), l, i, k, (e, _), i, t, _), (h, o, t), ((，, ↵), (s, o, m, (e, _), l, i, k, (e, _), i, t, _)), (c, (o, l, d)), ((，, ↵), (s, o, m, (e, _), l, i, k, (e, _), i, t, _)), ((i, n), _, t, h, ((e, _), p, o), t, (，, ↵), n, (i, n), (e, _), d, a, y, s, _, (o, l, d), .));"""

main(newick_str)

 Output is:

[Jaime Huerta Cepas]

nice! thanks for sharing

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