plotNetwork: Plot Network Graph

In CIDER: Meta-Clustering for scRNA-Seq Integration and Evaluation

Plot Network Graph

Description

Visualise the network based on 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,
  batch.var = "Batch",
  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.
batch.var	Character. Metadata colname containing batch information. (Default: Batch)
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

CIDER documentation built on April 4, 2025, 2:28 a.m.