plotNetwork {CIDER}R Documentation

Plot Network Graph

Description

Network visualisation for an IDER-based similarity matrix. The vertexes are initial clusters, and the edge width denotes the similarity between two initial clusters.

Usage

plotNetwork(
  seu,
  ider,
  colour.by = NULL,
  weight.factor = 6.5,
  col.vector = NULL,
  vertex.size = 1
)

Arguments

seu

Seurat S4 object after the step of 'getIDER', containing 'initial_cluster' and 'Batch' in its meta.data. Required.

ider

A list. Output of 'getIDER'. Required.

colour.by

Character. It should be one of the colnames of Seurat object meta.data.It is used to colour the vertex of the network graph. (Default: NULL)

weight.factor

Numerical. Adjust the thickness of the edges. (Default: 6.5)

col.vector

A vector of Hex colour codes. If no value is given (default), a vector of 74 colours will be used.

vertex.size

Numerical. Adjsut the size of vertexes. (Default: 1)

Value

An igraph object

See Also

getIDEr graph_from_data_frame


[Package CIDER version 0.99.1 Index]