Using custom colours for embedding

[AAA-3]

Hello!

I am imported a colour palette from my Seurat file and stored the colours in the same order as the clusters:

In trying to use those colours to label my clusters,:

scv.pl.velocity_embedding_stream(WT, basis='tsne', color='Clustername', legend_loc='right margin', palette=WT.uns['ClusterName_colors'])

I get this warning:

How can I call my seurat colours in scvelo? I checked #103 and #183 but it doesn't seem to work...

Versions:

scvelo==0.2.3 scanpy==1.8.1 anndata==0.7.6 loompy==3.0.6 numpy==1.21.2 scipy==1.6.3 matplotlib==3.4.3 sklearn==0.24.2 pandas==1.3.2

Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
ERROR: XMLRPC request failed [code: -32500]
RuntimeError: PyPI's XMLRPC API is currently disabled due to unmanageable load and will be deprecated in the near future. See https://status.python.org/ for more information.

[WeilerP]

@AAA-3, you don't set the argument palette. You simply need to specify the column name by which to color the scatter plot. The colors are inferred automatically.

Note: Running your cell changes the value of adata.uns['ClusterName_colors']. Consequently, to color the embedding with your original colors, you need to reload the data and remove the argument palette.

[AAA-3]

When I reloaded the data and ran the code:
scv.pl.velocity_embedding_stream(WT, basis='tsne', color='Clustername', legend_loc='right margin')
I got the same output. I doublechecked my colours as well and they were in the correct order (same as above)

The colours I expect (not in the same order as the adata):

[WeilerP]

@AAA-3, would you please change the field name in adata.uns from 'ClusterName_colors' to 'Clustername_colors' and check the result?

[AAA-3]

Worked! Thanks :D