Hello , i’m wondering if i can use the seurat weigted nearest neighbord graph based on two modalities RNA and ATAC to create Force-directed graph . That way the graph will likely represent both omics instead of one. Did it make sens biologically ?
thank you !
Sure, you can do this with muon.pp.neighbors function, which computes a WNN graph on top of the modalities in a MuData object.
Here’s a tutorial on using it: CITE-seq data integration with weighted nearest neighbours — muon-tutorials documentation
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thank you ! it seems to be just what i needed