Add a figure object to AxesSubplot Gridspec

Question

I am using Biopython's Phylo module to generate a tree, and further used gcf to save this current tree as a figure object of matplotlib.

tree = Phylo.read("my tree.nwk", "newick")  
Phylo.draw(tree)
tree_f=plt.gcf()

I want to be able to make use of this figure object in a subplot:

gs = gridspec.GridSpec(1, 2, height_ratios=[1, 1, -2, 2],
                             width_ratios=[1, 1, -2, 2], hspace=0, wspace=0) 
phyl_ax = plt.subplot(gs[0])
ht_ax = plt.subplot(gs[1])

How do I make phyl_ax take up a figure object?

I have tried phyl_ax(tree_f), but this fails with:

TypeError: 'AxesSubplot' object is not callable.

Answer 1

I haven't used Phylo, but from the documentation it looks like you just need to set your axes as a keyword:

phyl_ax=plt.subplot(gs[0])   
Phylo.draw(tree, axes=phyl_ax)