edgesFromDM: Create an edge list from the transition matrix of the...

In farrellja/URD: URD

Description

Returns a list of edges with transition probability from the diffusion map in an URD object. Used by some plotting functions to show the connectivity of the network if desired.

Usage

edgesFromDM(
  object,
  cells = NULL,
  include.connected.cells = F,
  edges.return = NULL
)

Arguments

object	An URD object
cells	(Character vector) Cells to calculate edges between (default NULL uses all cells in diffusion map.)
include.connected.cells	(Logical) If FALSE, then only edges that connect two cells included in cells will be kept. If TRUE, then edges where at least one connected cell is in cells will be kept.
edges.return	(Numeric) Number of edges to return (default NULL returns all edges.)

Value

A data.frame with columns from (cell name), to (cell name), and weight (transition probability)

Examples

edges <- edgesFromDM(object, cells=NULL, edges.return=100000)

farrellja/URD documentation built on June 17, 2020, 4:48 a.m.