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