RunModuleUMAP: RunModuleUMAP

In smorabit/hdWGCNA: hdWGCNA

RunModuleUMAP

Description

Run UMAP on co-expression matrix using hub genes as features.

Usage

RunModuleUMAP(
  seurat_obj,
  n_hubs = 10,
  exclude_grey = TRUE,
  genes_use = NULL,
  wgcna_name = NULL,
  n_neighbors = 25,
  metric = "cosine",
  spread = 1,
  min_dist = 0.4,
  supervised = FALSE,
  ...
)

Arguments

seurat_obj	A Seurat object
n_hubs	number of hub genes to use in the UMAP computation
exclude_grey	logical indicating whether to include grey module
genes_use	character vector of genes to use for the UMAP, must already be present in GetModules(seurat_obj)
wgcna_name	The name of the hdWGCNA experiment in the seurat_obj@misc slot
...	Additional parameters supplied to uwot::umap

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