ModuleUMAPPlot: ModuleUMAPPlot

In smorabit/hdWGCNA: hdWGCNA

ModuleUMAPPlot

Description

Makes a igraph network plot using the module UMAP

Usage

ModuleUMAPPlot(
  seurat_obj,
  sample_edges = TRUE,
  edge_prop = 0.2,
  label_hubs = 5,
  edge.alpha = 0.25,
  vertex.label.cex = 0.5,
  label_genes = NULL,
  return_graph = FALSE,
  keep_grey_edges = TRUE,
  wgcna_name = NULL,
  ...
)

Arguments

seurat_obj	A Seurat object
sample_edges	logical determining whether we downsample edges for plotting (TRUE), or take the strongst edges.
edge_prop	proportion of edges to plot. If sample_edges=FALSE, the strongest edges are selected.
label_hubs	the number of hub genes to label in each module
edge.alpha	scaling factor for edge opacity
vertex.label.cex	font size for labeled genes
return_graph	logical determining whether to plot thr graph (FALSE) or return the igraph object (TRUE)
keep_grey_edges	logical determining whether to show edges between genes in different modules (grey edges)
wgcna_name	The name of the hdWGCNA experiment in the seurat_obj@misc slot

Examples

ModuleUMAPPlot

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