a suggestion of save parameter in _chromosome_heatmap.py

[champeil]

Description of feature

When I want to save the heatmap with infercnv.pl.chromosome_heatmap, I noticed about I can't not specify the position to save the heatmap. May be the save parameter can be modified to better specify the position to save?

[grst]

This is a known issue with scanpy: scverse/scanpy#1508 (comment) (chromosome_heatmap internally calls scanpy.pl.heatmap)

But the following should work:

import matplotlib.pyplot as plt

fig, ax = plt.subplots(figsize=(10, 5))
infercnv.pl.chromosome_heatmap(..., ax=ax)
fig.figsave("/where/ever/heatmap.pdf")

[champeil]

I tried with the suggestion, but it return error:

  File "infercnv.py", line 66, in <module>
    cnv.pl.chromosome_heatmap(df, groupby="Cluster", dendrogram=True, ax=ax)
  File "singlecell/lib/python3.8/site-packages/infercnvpy/pl/_chromosome_heatmap.py", line 75, in chromosome_heatmap
    return_ax_dic = sc.pl.heatmap(
  File "singlecell/lib/python3.8/site-packages/scanpy/plotting/_anndata.py", line 1177, in heatmap
    im = heatmap_ax.imshow(obs_tidy.values, aspect='auto', norm=norm, **kwds)
TypeError: inner() got multiple values for argument 'ax'

here is my code:

fig, ax = plt.subplots(figsize=(12, 8))
cnv.pl.chromosome_heatmap(df, groupby="Cluster", dendrogram=True, ax=ax)
fig.figsave(args.result_dir+"/"+args.name+"_cnv_pheatmap.pdf")

[grst]

Sorry, I was wrong. This doesn't work because sc.pl.heatmap requires multiple ax objects.

What does work is the following though:

axs = cnv.pl.chromosome_heatmap(adata, groupby="cell_type", show=False)
axs["heatmap_ax"].get_figure().savefig("/path/to/plot.pdf")

[grst]

Closing this, because this is more of a scanpy issue and there's a workaround.