cluster functional terms into groups by clustering the similarity matrix of the terms

Source: R/Plots.R

We utilize package simplifyEnrichment to cluster GO terms into groups from the semantic similarity matrix. Summaries of GO terms in each cluster are visualized by word clouds. https://bioconductor.org/packages/release/bioc/html/simplifyEnrichment.html https://bioconductor.org/packages/release/bioc/vignettes/simplifyEnrichment/inst/doc/simplifyEnrichment.html package "simplifyEnrichment" is developed based on R version 4.0

simplifyEnrichmentplot(
  SeuratObj,
  by = "GO",
  pathwayIDs = NULL,
  showCategory = 10,
  GO_ont = "BP"
)

Arguments

SeuratObj

Seurat object
by

GO, KEGG, Reactome, MSigDb
pathwayIDs

a vector of pathway IDs, such as a vector of GO IDs
showCategory

number of top pathways of each cluster
GO_ont

Gene Ontology

Examples

if (FALSE) {
simplifyEnrichmentplot(SeuratObj, by = "GO", showCategory = 10)
}