Unable to change vmax in scanpy.pl.scatter

[alm8517]

Hi Scanpy team,

A potentially silly question. I'm having problems changing vmax in sc.pl.scatter.

I want to set 'dpt_pseudotime' vmax to 0.5, similar to how vmax and vmin can be changed, for example, in sc.pl.umap.

I tried the following:

with axes_style({'axes.grid': False}):
sc.pl.scatter(adata_0_1, x='Vim', y='Lyz2', color='dpt_pseudotime', size=5, use_raw=False,
color_map='RdYlBu_r', vmax=0.5)

But get the following error:

I read in the scanpy.pl.scatter documentation that kwargs can be used to set vmax. I tried this approach, but got the same result as above:

kwargs={'vmax':0.5}

with axes_style({'axes.grid': False}):
sc.pl.scatter(adata_0_1, x='Vim', y='Lyz2',
color='dpt_pseudotime', size=5, use_raw=False, color_map='RdYlBu_r', **kwargs)

I tried to find a solution online with no success. Any help/suggestions will be appreciated

P.S: This is my first post and I'm a huge fan of your package. Keep up the great work!

[flying-sheep]

Hi! thank you for the praise! I’m afraid this is a documentation bug!

We had a bit of an issue with documented parameters not matching real ones. It’s fixed in the latest docs where scatter doesn’t say it has a kwargs or vmax parameter.

We should simplify our plotting. @VolkerBergen has some nice plotting functions, but implemented them as part of scvelo, not scanpy as he should have 😜

[VolkerBergen]

Soonish! ;) For now, you can do that through scvelo (scvelo.org) in analogy to scanpy with
scv.pl.scatter(adata, ..., vmax=.5).

There's probably also a way to manually set pl.clim() or ax.set_clim() in scanpy..

[flying-sheep]

Soonish!

awesome!

There's probably also a way […]

Yeah, the function should return an Axes object (at least if show=False, but idk why it doesn’t just always returns that)