FindRootCell: Find the root cell

In mkarikom/RSoptSC: Low-Rank Factorization for Subspace-clustering

Find the root cell

Description

Use either the primary manifold embedding of cell similarity to find the root cell by cluster-cell rank-correlation or use the flattened representation of this embedding to find the root cell by maximum separation heuristic. Possible values for cluster_order_by are predecessor and distance. Possible values for cell_order_by are index and distance.

Usage

FindRootCell(
  use_flat_dist = TRUE,
  cluster_order_by = "distance",
  cell_order_by = "distance",
  graph_cluster_mst = NULL,
  dist_graph = NULL,
  dist_flat,
  cluster_labels = NULL,
  root_cluster = NULL
)

Arguments

use_flat_dist	use max path length heuristic on flat embedding
cluster_order_by	cluster rank parameter for measuring cluster/cell rank correlation
cell_order_by	cell-wise pseudotime parameter for measuring cluster/cell rank correlation
graph_cluster_mst	igraph object representing an mst on the cluster-cluster graph
dist_graph	a distance matrix of cells embedded in a graph
dist_flat	the manifold embedding of the cells
cluster_labels	the cluster label for each cell
root_cluster	the id of the root cluster on the cluster-cluster graph

Value

integer index of the root cell

mkarikom/RSoptSC documentation built on May 10, 2023, 1:10 a.m.