Small multiple plots for clusters

• Additional function parameters / changed functionality / changed defaults?
• New analysis tool: A simple analysis tool you have been using and are missing in sc.tools?
• New plotting function: A kind of plot you would like to seein sc.pl?
• External tools: Do you know an existing package that should go into sc.external.*?
• Other?

Hey @fidelram !

I just wrote something to create small multiples to plot cells in a clustering category. Pretty simple and very useful if you have too many clusters. What do you think of this:

def cluster_small_multiples(adata, clust_key, size=60, frameon=False, legend_loc=None, **kwargs):
    tmp = adata.copy()

    for i,clust in enumerate(adata.obs[clust_key].cat.categories):
        tmp.obs[clust] = adata.obs[clust_key].isin([clust]).astype('category')
        tmp.uns[clust+'_colors'] = ['#d3d3d3', adata.uns[clust_key+'_colors'][i]]

    sc.pl.umap(tmp, groups=tmp.obs[clust].cat.categories[1:].values, color=adata.obs[clust_key].cat.categories.tolist(), size=size, frameon=frameon, legend_loc=legend_loc, **kwargs)

Example output from:

test = sc.datasets.pbmc68k_reduced()
sc.pp.pca(test)
sc.pp.neighbors(test)
sc.tl.umap(test)
cluster_small_multiples(test, 'bulk_labels')

Could generalize this to different bases via sc.pl.scatter(). Or is this already implemented somewhere that I’m not aware of? Or maybe it’s too simple to have as a small helper function?

[VolkerBergen]

Any keyword suggestion? groups='all' as @gokceneraslan suggested?

[wangjiawen2013]

How are the things going now ?