Adding y_axis scale function

[NikiB]

The function gives the option to add full y axis scale to the tree in linear or log setting.
Also deleted the the twice written add_legend function in qt4_render.py (left one copy)
and set the script to fit better the pep8 structure

[jhcepas]

that's great. Thanks! I would review as soon as possible.
How does the y-axis scale look like? is the tree expected to rotate so the y-axis follows branch lengths? Maybe easier to understand if you can add a screenshot. I can not try the code right now..

[NikiB]

The scale rotates but only at 90/180/270 degrees (It looks graphically bad otherwise)
I'll add my basic code here and a screenshot.

[NikiB]

import os
import math
import matplotlib.pyplot as plt

%matplotlib notebook

os.environ["DISPLAY"] = ':4'
import ete3

t_f= '(((Leaf 32:1,Leaf 31:1):0.5,(Leaf 22:1,Leaf 21:1):11,(Leaf 2:1,Leaf 1:1):11,(Leaf 3:1,Leaf 4:1):12):11,(Leaf 5:1,Leaf 6:1):24);'
t_r = ete3.Tree(newick=t_f, format=1)

tss = ete3.TreeStyle()
tss.show_scale = False

t1 = ete3.TextFace("Header Face", fsize=12, fgcolor='black')
t2 = ete3.TextFace("Footer Face", fsize=8, fgcolor='black')
tss.title.add_face(ete3.TextFace('tree_name', fsize=20), column=0)
tss.aligned_header.add_face(t1,0)

tss.aligned_foot.add_face(t2, column=-1)

for leaf in t_r:
leaf.add_face(ete3.TextFace('text1'), column=1, position='aligned')
leaf.add_face(ete3.TextFace('text2'), column=2, position='aligned')

tss.show_scale=True

tss.rotation = 90

tss.y_axis['scale_length'] = math.ceil(t_r.get_farthest_leaf()[1] - t_r.dist)
tss.y_axis['show'] = True

tss.y_axis['scale_type'] = 'log'

t_r.render("%%inline", tree_style=tss)

[jhcepas]

awesome, this is actually addressing #112
Note that when using this type of scale, node.img_style["size"] should be set to 0 in all internal nodes, otherwise tree length and the scale bar will not fit and align perfectly.

[NikiB]

yes, various node sizes will alter the results

[NikiB]

Hi, I added a function that resize the internal nodes to node.img_style["size"]=0 and adds a face the floats behind the nodes and doesn't alter the scale.

[NikiB]

Hi,
We have fixed qt_render to match qt5 and qt4 simultaneously and updated with the latest master.

[jhcepas]

thanks! I will need some time for testing. Could you add some test code in ete/ete3/test/test_treeview/test_all_treeview.py. It is not the most elegant way of testing the rendering, but at least allows to check at a glance that graphic features are working ok...