There is something I don't understand in Bio.Phylo, when we do :
from Bio import Phylo
tree = Phylo.read("my_tree","newick")
tree_plot = Phylo.draw(tree)
EDIT :
$ cat my_tree
(((A,B),C),D)
tree_plot is Nonetype because Phylo.draw() doesn't return anything. The 2 last lines of the source code are :
if do_show:
plt.show()
I would like to interact with the tree, and add for instance a dot in front of some of the tree leaves. So I added in the source code on my computer at the last line :
if do_show:
plt.show()
return axes
now, with the piece of code I write at the beginning, I have in tree_plot:
In [1]: type(tree_plot)
Out[1]: matplotlib.axes.AxesSubplot
And I'm now able to access data from the tree with for instance :
In [2]: tree_plot.texts
Out[2]: [<matplotlib.text.Text at 0x114d02710>,
<matplotlib.text.Text at 0x114d02990>,
<matplotlib.text.Text at 0x114d02ed0>,
<matplotlib.text.Text at 0x114d00cd0>,
<matplotlib.text.Text at 0x114d3c410>,
<matplotlib.text.Text at 0x114d3cb10>]
or plotting a line with :
tree_plot.plot(range(10))
And so on with any other axes.AxesSubplot method.
Why is there no return
statement in the Phylo.draw()
function ? If it's on purpose, why and how one can draw something on the same axis ?
I'm using
Thanks
Why they don't return the figure you will have to ask the developers (or maybe suggest the change). However it is quite easy to work around:
First make sure you have matplotlib
in interactive mode:
from matplotlib import pyplot as plt
plt.ion()
Then run your:
Phylo.draw(tree)
After that if you just want the ax
, to add some text you use
ax = plt.gca()
ax.text(1, 4, "Hello World")
plt.show()
Or if you want the whole figure use plt.gcf()
. Remember to do plt.show()
to see your updates.
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