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visualize seurat(RDS format) with cirrocumulus #177

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wang0430 opened this issue Mar 23, 2023 · 1 comment
Open

visualize seurat(RDS format) with cirrocumulus #177

wang0430 opened this issue Mar 23, 2023 · 1 comment

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@wang0430
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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
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How did you convert the Seurat file to h5ad? It looks like the conversion process didn't save your cluster labels as categorical.

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@joshua-gould @wang0430