GSEAplot: GSEA plot

In huayc09/SeuratExtend: SeuratExtend

GSEA plot

Description

Generate plot that mimic the Gene Set Enrichment computational analysis published by the Broad Institute

Usage

GSEAplot(
  seu,
  group.by = NULL,
  geneset,
  ident.1 = NULL,
  ident.2 = NULL,
  cells = NULL,
  slot = "data",
  assay = NULL,
  logFC.cutoff = c(-1, 1),
  p.position = c(0.8, 0.85),
  sample = 500,
  title = deparse(substitute(geneset))
)

Arguments

seu	Seurat object
group.by	A variable name in meta.data to group the violin plots by, or string with the same length of cells
geneset	A list of genes
ident.1	Cell type name
ident.2	(Optional) Second cell type name to compare with 'ident.1'
cells	Cell names to use, Default: all cells
slot	Slot to pull feature data for, Default: 'data'
assay	Name of assay to use, defaults to the active assay
logFC.cutoff	Range of Log2 fold change of ranked genes, Default: c(-1, 1)
p.position	Where to put ES and p value text, Default: c(0.8, 0.85)
sample	Points used for drawing curves. Default: 500
title	Title of geneset

Details

P value is calculated using Kolmogorov-Smirnov Tests

Value

Plot

Examples

GSEAplot(
  pbmc, ident.1 = "CD4 T Naive", title = "INTERFERON_GAMMA_RESPONSE",
  geneset = hall50$human$HALLMARK_INTERFERON_GAMMA_RESPONSE)

huayc09/SeuratExtend documentation built on July 15, 2024, 6:22 p.m.