irGSEA.vlnplot: Half vlnplot

In chuiqin/irGSEA: The integration of single cell rank-based gene set enrichment analysis

Half vlnplot

Description

Easy to show the data distribution by half vlnplot

Usage

irGSEA.vlnplot(
  object = NULL,
  method = NULL,
  show.geneset = NULL,
  group.by = NULL,
  color.cluster = NULL,
  cluster.levels = NULL
)

Arguments

object	A Seurat after perform irGSEA.score
method	A character. It should be one or more of the followling : AUCell, UCell, singscore, ssgsea, JASMINE, VAM, scSE, VISION, gficf, GSVA, zscore, plage, wmean, wsum, mdt, viper, GSVApy, AddModuleScore, pagoda2.
show.geneset	A character. It should be one of the rownames of enrichment score matrix.
group.by	Default ident when it is set to NULL. You can specify other column of metadata.
color.cluster	A vector. Default "ggsci::pal_igv()(the number of colnames of enrichment score matrix)" when it is set to NULL.
cluster.levels	A vector equal to the number of clusters.

Value

vlnplot

Examples

## Not run: 
# 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')

irGSEA.vlnplot.plot1 <- irGSEA.vlnplot(object = pbmc3k.final,
method = c("AUCell", "UCell", "singscore", "ssgsea"),
show.geneset = "HALLMARK-INFLAMMATORY-RESPONSE")
irGSEA.vlnplot.plot2 <- irGSEA.vlnplot(object = pbmc3k.final,
method = c("AUCell", "UCell", "singscore", "ssgsea"),
show.geneset = "HALLMARK-IL6-JAK-STAT3-SIGNALING")



## End(Not run)

chuiqin/irGSEA documentation built on July 27, 2024, 6:27 a.m.