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Determining cluster order for colouring

See original GitHub issue

Hey!

I am attempting to visualise velocity on top of a seurat generated clusters, displayed as a UMAP, which has worked, however I am having difficulty syncing the colours between what I’ve made in Seurat, with the scvelo output.

My approach was to extract the colours from seurat, and use them as the palette variable (as below). However the clusters in the output are coloured in the wrong order (I imagine the order may have been lost when merging the loom files?). I’ve looked through my adata’s metadata but can’t find a cluster order that matches the output.

How do I extract the cluster order that scvelo uses for colouring so I can re-order my palette variable accordingly?

Thanks!

ident_colours = ['#F8766D','#E18A00','#BE9C00','#8CAB00','#24B700','#00BE70','#00C1AB','#00BBDA','#00ACFC','#8B93FF','#D575FE','#F962DD','#FF65AC']

scv.pl.velocity_embedding_stream(adata, basis = "X_umap_cell_embeddings", color = "ClusterName", palette = ident_colours)

Issue Analytics

State:
Created 4 years ago
Comments:7 (2 by maintainers)

Top GitHub Comments

1reaction

GBeattiecommented, Nov 11, 2019

Sorted! Somewhere in the processing seurat’s ordering has been changed, just had to manually reorder the colours to match. Thank you for the assistance!

1reaction

VolkerBergencommented, Nov 11, 2019

You can access the ordered cluster labels and corresponding color codes with adata.obs['ClusterName'].cat.categories and adata.uns['ClusterName_colors'], assuming that you have the clusters stored in adata.obs['ClusterName'].

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