getClusterGraph: Collapse vertices belonging to each cluster in a graph

In kharchenkolab/sccore: Core Utilities for Single-Cell RNA-Seq

Collapse vertices belonging to each cluster in a graph

Description

Collapse vertices belonging to each cluster in a graph

Usage

getClusterGraph(
  graph,
  groups,
  method = "sum",
  plot = FALSE,
  node.scale = 50,
  edge.scale = 50,
  edge.alpha = 0.3,
  seed = 1,
  ...
)

Arguments

graph	igraph graph object Graph to be collapsed
groups	factor on vertices describing cluster assignment (can specify integer vertex ids, or character vertex names which will be matched)
method	string Method to be used, either "sum" or "paga" (default="sum")
plot	boolean Whether to show collapsed graph plot (default=FALSE)
node.scale	numeric Scaling to control value of 'vertex.size' in plot.igraph() (default=50)
edge.scale	numeric Scaling to control value of 'edge.width' in plot.igraph() (default=50)
edge.alpha	numeric Scaling to control value of 'alpha.f' in adjustcolor() within plot.igraph() (default=0.3)
seed	numeric Set seed via set.seed() for plotting (default=1)
...	arguments passed to collapseGraphSum()

Value

collapsed graph

Examples

cluster.graph = getClusterGraph(conosGraph, igraph::V(conosGraph))

kharchenkolab/sccore documentation built on June 2, 2025, 12:43 p.m.