GSEA plot

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

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

Value

Plot

Details

P value is calculated using Kolmogorov-Smirnov Tests

Examples

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