retrieveRefClusters {phemd} | R Documentation |
Takes initial Phemd struct and returns cell clusters as assigned by clustering algorithm (e.g. PHATE or Monocle2)
retrieveRefClusters( obj, cell_model = c("monocle2", "seurat", "phate"), expn_type = "reduced", ndim = 10 )
obj |
Phemd struct containing cell-state embedding object and underlying expression data |
cell_model |
String representing data model for cell-state space ("seurat", "monocle2", or "phate") |
expn_type |
String representing whether to return raw expression values or coordinates in dimensionality-reduced feature space |
ndim |
Number of dimensions in reduced dimensionality space (e.g. PHATE / CCA) to use (only relevant in reduced dimensionality space) |
Private method (not exported in namespace)
List of data matrices; each list element is of size num_cells_in_cluster x num_markers and represents a distinct cell cluster
## Not run: cluster_expression_data <- retrieveRefClusters(my_phemdObj) ## End(Not run)