Straightforward way for getting most abundant categories #51
Description
In GitLab by @grst on Mar 31, 2020, 16:52
We need it regulary to get the top n of a category, e.g. v-gene or clonotype.
This can be achieved in a pandas onliner, if one knows how to do it...
# This is probably hacky, we might think about a better way, but we need the most abundant clonotypes
top_clonotypes = adata.obs.clonotype.value_counts()[:8].index.values.tolist() # A better way might be needed especailly to take normalization into account
top_vgenes = adata.obs.TRB_1_v_gene.value_counts()[:8].index.values.tolist()It would be more user-friendly to have a convenience function to this,
for instance:
ir.tl.top_clonotypes(n=10)
ir.tl.top_genes(gene="V", chain="TRA_1")or maybe even more flexible
ir.tl.top_n(col="clonotype", n=10)Use it for plotting:
sc.pl.umap(adata, color="clonotype", groups=ir.tl.top_n("clonotype", 10))@szabogtamas, what do you think of this approach?
This could actually become a scanpy feature as it's not scirpy specific.