circle plot of clusters

Helps to infer the relationship between clusters. Link width shows Pearson correlation or Jaccard coefficient between clusters, calculated with GSEA result. Node size indicates cell number of each cluster. If by = "GO" and pathwayIDs = NULL, only GO terms of level 5-6 are used for calculation.

clustercorplot(
  SeuratObj,
  by = "GO",
  pathwayIDs = NULL,
  color.use = NULL,
  weight.scale = TRUE,
  label.edge = FALSE,
  edge.curved = 0.2,
  shape = "circle",
  layout = igraph::in_circle(),
  margin = 0.1,
  vertex.size.cex = 1,
  link_threshold = 0.5,
  vertex.label.cex = 1.5,
  vertex.label.color = "black",
  arrow.width = 1,
  arrow.size = 0.2,
  edge.label.color = "black",
  edge.label.cex = 0.5,
  edge.max.width = 8,
  vertex.label.dist = 2
)

clustercorplot_jaccard(
  SeuratObj,
  by = "GO",
  pathwayIDs = NULL,
  color.use = NULL,
  weight.scale = TRUE,
  label.edge = FALSE,
  edge.curved = 0.2,
  shape = "circle",
  layout = in_circle(),
  margin = 0.1,
  vertex.size.cex = 1,
  link_threshold = 0.4,
  vertex.label.cex = 1.5,
  vertex.label.color = "black",
  arrow.width = 1,
  arrow.size = 0.2,
  edge.label.color = "black",
  edge.label.cex = 0.5,
  edge.max.width = 8,
  vertex.label.dist = 2
)

Arguments

SeuratObj	Seurat object
by	which GSEA result to use for calculation
pathwayIDs	IDs of pathways to use for calculation
color.use	used to color nodes, can be a named vector
weight.scale	scale the width or not
label.edge	label edges or not
edge.curved	The degree of edge bending
shape	shape of nodes, 'circle' by default
layout	network layout, circle by default
margin	margin of plot
vertex.size.cex	node size
link_threshold	only show links whose correlation/Jaccard-index bigger than this threshold
vertex.label.cex	size of node label
vertex.label.color	color of label of nodes, 'black' by default
arrow.width	width of arrow
arrow.size	size of arrow
edge.label.color	color of label of edge, 'black' by default
edge.label.cex	size of edge label
edge.max.width	width of edge
vertex.label.dist	distance between label and nodes

Examples

if (FALSE) {
# show Pearson correlation between clusters
clustercorplot(SeuratObj, by = "GO")
}


if (FALSE) {
# show Jaccard coefficient between clusters
clustercorplot_jaccard(SeuratObj, by = "GO")
}