How to map all the cell type in a single visium slide

almaan / stereoscope

Spatial mapping of cell types by integration of transcriptomics data

MIT License

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How to map all the cell type in a single visium slide #33

Open AkilaRanjith opened 1 year ago

AkilaRanjith commented 1 year ago

Hello All,

Thanks for the steroscope cool method!!! It lloks pretty good for my data.

I need some help to plot all my celltype in the spatial data and get single image. I used scatter plot but still another way to get nice plot plt.scatter(sl_adata.obsm["spatial"][:, 0], sl_adata.obsm["spatial"][:, 1], c=sl_adata.obsm["deconvolution"].values.argmax(1), cmap="Set2")