Bubble plot — irGSEA.bubble • irGSEA

Easy to show analysis results by bubble plot

irGSEA.bubble(
  object = NULL,
  method = "RRA",
  top = 50,
  show.geneset = NULL,
  cluster.color = NULL,
  direction.color = NULL,
  significance.color = NULL,
  cluster_rows = T,
  cluster.levels = NULL
)

Arguments

object: A list after perform irGSEA.integrate
method: A character. It should be one of the followling : AUCell, UCell, singscore, ssgsea or RRA. Default RRA.
top: The top gene sets. Default 50.
show.geneset: A vector including special gene sets. Default NULL.
cluster.color: A vector. Default "ggsci::pal_igv()(the number of colnames of enrichment score matrix)" when it is set to NULL.
direction.color: A vector. Default "c("#4575B4","#D73027")" when it is set to NULL.
significance.color: A vector. Default "c("#D0DFE6FF","#f87669")" when it is set to NULL.
cluster_rows: Whether to make cluster on rows. Defaul True.
cluster.levels: A vector equal to the number of clusters.

Value

bubble plot

Examples

if (FALSE) {
# load PBMC dataset by R package SeuratData
library(Seurat)
library(SeuratData)
# download 3k PBMCs from 10X Genomics
InstallData("pbmc3k")
data("pbmc3k.final")
pbmc3k.final <- SeuratObject::UpdateSeuratObject(pbmc3k.final)

# Seurat object
pbmc3k.final <- irGSEA.score(object = pbmc3k.final, assay = "RNA",
slot = "data", msigdb = T, species = "Homo sapiens",
category = "H", geneid = "symbol",
method = c("AUCell", "UCell", "singscore", "ssgsea"), kcdf = 'Gaussian')

# Integrated analysis
result.dge <- irGSEA.integrate(object = pbmc3k.final,
group.by = "seurat_annotations", metadata = NULL, col.name = NULL,
method = c("AUCell","UCell","singscore","ssgsea"))

irGSEA.bubble.plot1 <- irGSEA.bubble(object = result.dge,
method = "RRA", top = 50)
irGSEA.bubble.plot2 <- irGSEA.bubble(object = result.dge,
method = "ssgsea", top = 50)

}