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)