irGSEA.density.scatterplot: Density Scatter plot

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

Density Scatter plot

Description

Easy to the data distribution by density scatter plot

Usage

irGSEA.density.scatterplot(
  object = NULL,
  method = NULL,
  show.geneset = NULL,
  reduction = "umap",
  ...
)

Arguments

object	A Seurat after perform irGSEA.score
method	A character. It should be one of the followling : AUCell, UCell, singscore, ssgsea.
show.geneset	A character. It should be one of the rownames of enrichment score matrix.
reduction	A character. It can not be empty and should be calculated in advance.
...	More parameters pass to plot_density

Value

density scatter plot

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.density.scatterplot1 <- irGSEA.density.scatterplot(object = pbmc3k.final,
method = "UCell", show.geneset = "HALLMARK-INFLAMMATORY-RESPONSE",
reduction = "umap")
irGSEA.density.scatterplot2 <- irGSEA.density.scatterplot(object = pbmc3k.final,
method = "ssgsea", show.geneset = "HALLMARK-IL6-JAK-STAT3-SIGNALING",
reduction = "umap")


## End(Not run)

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