R: Collapse vertices belonging to each cluster in a graph

getClusterGraph {sccore} | R Documentation

## 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))

[Package sccore version 1.0.1 Index]