sccore: getClusterGraph – R documentation

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getClusterGraph

Collapse vertices belonging to each cluster in a graph

Collapse vertices belonging to each cluster in a graph

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

`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()

collapsed graph

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

Core Utilities for Single-Cell RNA-Seq

v0.1.3

GPL-3

Authors

Viktor Petukhov [aut], Ramus Rydbirk [aut], Peter Kharchenko [aut], Evan Biederstedt [aut, cre]

Initial release