show embedded histogram or pie chart on UMAP/TSNE plot

Source: R/Plots.R

embedded histogram or pie chart show pathway GSEA score on each clusters. If by = "GO" and pathwayIDs = NULL, only GO terms of level 5-6 are used for calculation.

embeddedplot(
  SeuratObj,
  by = "GO",
  pathwayIDs = NULL,
  topaths = 1,
  reduction = "umap",
  type = "pie",
  pie.size.cex = 1
)

Arguments

SeuratObj

Object of class "Seurat"
by

which GSEA result to show
pathwayIDs

IDs of pathways to show, if provided, parameter topaths become invalid.
topaths

number of top pathways of each cluster to show
reduction

"umap", "tsne", "pca"
type

"hist", "pie", type of embedded plots
pie.size.cex

size of pie chart

Examples

if (FALSE) {
embeddedplot(SeuratObj, type = "pie")
embeddedplot(SeuratObj, topaths = 3, reduction = "tsne", type = "hist")
}