RunModuleUMAP — RunModuleUMAP • hdWGCNA

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

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