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BlishLab / scriabin

Analysis of cell-cell communication at single-cell resolution
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group.by is Cell Type Column in Vignette #21

Open DarioS opened 4 months ago

DarioS commented 4 months ago

Note: we recommend using Scriabin's CCIM workflow to analyze pairs of that were actually capable of interacting in reality. group.by: Meta.data column name defining samples into which object should be split.

Why does the vignette split the data set by cell type? Wouldn't it make more sense to split by sample identifier?

FindAllInteractionPrograms(panc_id, iterate.threshold = 300, group.by = "celltype", assay = "alra", sim_threshold = 0.4)

If the Seurat object is split by cell type rather than by sample, there will be no interactions between different cell types, no? Is the best way group.by = "orig.ident", cell_types = "celltype" because cell_types is passed into InteractionPrograms via ...?