MetaspotsByGroups

Computes metaspots in a given Seurat object containing spatial transcriptomics data.

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