MetaspotsByGroups: MetaspotsByGroups

In smorabit/hdWGCNA: hdWGCNA

MetaspotsByGroups

Description

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

smorabit/hdWGCNA documentation built on Oct. 23, 2024, 11:19 p.m.