GSVA_pheatmap: This function is used to perform GSVA analysis

In Lian-Lab/LIANLAB: To integrate analysis methods and simplify analysis process

Description

This function is used to perform GSVA analysis

Usage

GSVA_pheatmap(
  em = NULL,
  seurat_object = NULL,
  gspath = NULL,
  species = "human",
  text.size = 2,
  topn = 20,
  min.sz = 2,
  filename = "geneset",
  clusters = NULL,
  pathname = NULL,
  width = 6,
  height = 5
)

Arguments

em	expression matrix as genes in row, samples or cells in column
seurat_object	it also support a seurat_object instead of expression matrix
gspath	the correct path of your geneset file(.gmt)
species	species of the seurat.obj or matrix
text.size	the size of the text
topn	number of the top pathways
min.sz	minimum size of the resulting gene sets
filename	the name of the generated file
clusters	to choose the clusters you interested
pathname	to choose the pathways you interested
width	the width of the figure
height	the heigh of the figure

Details

This function is used to perform GSVA analysis, including pheatmap part which exhibit the GSVA score of selected genesets in every samples or cells barplot part which exhibit the top20 different expressed genesets in two group

Examples

## Not run: 
input.file <- system.file('extdata','pbmc_1k.RDS',package = 'LIANLABDATA')
pbmc_1k <- readRDS(input.file)
GSVA_pheatmap(pbmc_1k,species="mouse")

## End(Not run)

Lian-Lab/LIANLAB documentation built on June 23, 2021, 5:37 a.m.