irGSEA.heatmap: Heatmap plot

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

Heatmap plot

Description

Easy to show analysis results by heatmap plot

Usage

irGSEA.heatmap(
  object = NULL,
  method = "RRA",
  top = 50,
  show.geneset = NULL,
  cluster_rows = T,
  significance.color = NULL,
  cluster.color = NULL,
  direction.color = NULL,
  rowname.fointsize = 7,
  heatmap.width = 17,
  heatmap.heigh = 13,
  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_rows	Whether to make cluster on rows. Defaul True.
significance.color	A vector. Default "c("#D0DFE6FF","#f87669")" when it is set to 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.
rowname.fointsize	The fointsize of rownames. Default 7.
heatmap.width	Width of the whole heatmap (including heatmap components), default 17.
heatmap.heigh	Height of the whole heatmap (including heatmap components), default 13.
cluster.levels	A vector equal to the number of clusters.
...	More parameters pass to Heatmap

Value

heatmap 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')

# 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.heatmap.plot1 <- irGSEA.heatmap(object = result.dge, method = "RRA",
top = 50, show.geneset = NULL)

irGSEA.heatmap.plot2 <- irGSEA.heatmap(object = result.dge, method = "ssgsea",
top = 50, show.geneset = NULL)


## End(Not run)

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