circle plot of clusters

Source: R/Plots.R

Link width shows number of intersection of pathways between clusters, link color is in concordance with cluster which has higher enrichment score on intersection pathways.

circleplot(
  SeuratObj,
  by = "GO",
  pvaluecutoff = 0.01,
  pathwayIDs = NULL,
  link_threshold = 10
)

Arguments

SeuratObj

Seurat object
by

which GSEA result to use, one of "GO", "KEGG", "Reactome", "MSigDb", "WikiPathways", "DO", "NCG", "DGN"
pvaluecutoff

calculate link width with pathways lower than pvaluecutoff
pathwayIDs

pathway IDs to calculate link width
link_threshold

only show links whose intersection number bigger than this threshold

Examples

if (FALSE) {
circleplot(SeuratObj, by = "GO", pvaluecutoff = 0.01, pathwayIDs = NULL)
}