Transferring Seurat Cluster Colours for scVelo analysis

Question

[Megan]

HI! I have a question regarding importing UMAP projections from Seurat into scVelo. I have a scRNAseq dataset, analysed via CellRanger then Seurat to produce my Seurat object. This object, which I've run all my analysis on including clustering, has been imported into a jupyter notebook as a loom file, and scVelo used to perform RNA velocity analysis.My UMAP projections didn't transfer across in my loom file and I had to manually import them as a csv file. However, my cluster colours have not transferred across. The plots look otherwise fine, but I can't see how to fix the colors. At present, the UMAP projection is a random assortment of colours, with the cluster labels bunched up in the middle. Any ideas on how I can fix this?

[antonioggsousa]

Hi,

I did the same analysis following the instructions in this tutorial:

https://github.com/basilkhuder/Seurat-to-RNA-Velocity

It explains how to give the same colors used in Seurat.

Best,

António