show relationship between clusters and pathways — hierarchyplot

Hierarchical clustering of clusters and pathways according to GSEA result. If by = "GO" and pathwayIDs = NULL, only GO terms of level 5-6 are used for calculation.

hierarchyplot_tree(
  SeuratObj,
  by = "GO",
  pathwayIDs = NULL,
  topaths = 5,
  cluster_cutree_k = NULL,
  pathway_cutree_k = NULL,
  color.use.cluster = NULL,
  color.use.pathway = NULL,
  weight.scale = TRUE,
  vertex.size.cex = 1,
  vertex.label.cex = 0.9,
  edge.max.width = 3,
  vertex.label.color = "black",
  alpha.edge = 0.6
)

Arguments

SeuratObj	Object of class "Seurat"
by	which GSEA result to show
pathwayIDs	IDs of pathways to show
topaths	top n pathway of each cluster
cluster_cutree_k	the clusters are divided into k, based on the hierarchical clustering (using cutree)
pathway_cutree_k	the pathways are divided into k, based on the hierarchical clustering (using cutree)
color.use.cluster	used to color the cluster nodes, a named vector or a vector
color.use.pathway	used to color the pathway nodes
weight.scale	scale the width or not
vertex.size.cex	node size
vertex.label.cex	size of node label
edge.max.width	width of edge
vertex.label.color	color of label of nodes, 'black' by default
alpha.edge	transparency of edge color

Examples

if (FALSE) {
hierarchyplot_tree(SeuratObj, by = "GO", topaths = 10, cluster_cutree_k = 5, pathway_cutree_k = 20)
}