visualize seurat(RDS format) with cirrocumulus

lilab-bcb / cirrocumulus

Bring your single-cell data to life

https://cirrocumulus.readthedocs.io/

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visualize seurat(RDS format) with cirrocumulus #177

Open wang0430 opened 1 year ago

wang0430 commented 1 year ago

Hello, I'm running into a problem right now. I use Seurat to analyze spatial transcriptome data, and save it as an RDS file after dimensionality reduction clustering. I want to use cirrocumulus to visualize my data (RDS format). I convert the seurat file to H5AD format, and then use "cirro launch C: /Users/admin/Desktop/V1/sc.h5ad --spatial C:/Users/admin/Desktop/V1/spatial "Visualization. But there is a problem here, my Cluster label can't be displayed. 1679539866376

joshua-gould commented 1 year ago

How did you convert the Seurat file to h5ad? It looks like the conversion process didn't save your cluster labels as categorical.