Computes metaspots in a given Seurat object containing spatial transcriptomics data.
Usage
MetaspotsByGroups(
seurat_obj,
group.by = c("seurat_clusters"),
ident.group = "seurat_clusters",
assay = "Spatial",
slot = "counts",
layer = "counts",
mode = "sum",
min_spots = 50,
wgcna_name = NULL
)Arguments
- group.by
A character vector of Seurat metadata column names representing groups for which metacells will be computed.
- assay
Assay to extract data for aggregation. Default = 'Spatial'
- slot
Slot to extract data for aggregation. Default = 'counts'
- layer
Layer to extract data for aggregation. Default = 'counts'. Layer is used with Seurat v5 instead of slot.
- mode
determines how to make gene expression profiles for metacells from their constituent single cells. Options are "average" or "sum".
- min_spots
the minimum number of spots in a particular grouping to construct metaspots
- wgcna_name
name of the WGCNA experiment
- cur_seurat
A Seurat object