plotGeneSet: Plot gene set enrichment

In acidgenomics/acidgsea: Acid Genomics GSEA

Plot gene set enrichment

Description

Plot gene set enrichment

Usage

plotGeneSet(object, ...)

## S4 method for signature 'FgseaList'
plotGeneSet(
  object,
  collection,
  contrast,
  set,
  colors = c(line = "black", min = AcidPlots::purpleOrange(n = 2L)[[1L]], max =
    AcidPlots::purpleOrange(n = 2L)[[2L]], ticks = "black", yintercept = "black")
)

Arguments

object	Object.
collection	character(1). Gene set collection name. Typically refers to h (hallmark), c1-c7 collections from MSigDb. Can obtain using collectionNames() on FgseaList object.
contrast	character(1). Contrast name.
set	character(1). Gene set name, in a defined collection. For example, "HALLMARK_ADIPOGENESIS".
colors	character(5). Named character color vector indicating: Line color. Minimum (negative) threshold line color. Maximum (positive) threhsold color. Y intercept at origin color. Ticks color.
...	Additional arguments.

Value

ggplot.

Note

Updated 2023-08-15.

See Also

Modified version of fgsea::plotEnrichment().

Examples

data(fgsea)

## FgseaList ====
object <- fgsea
contrast <- contrastNames(object)[[1L]]
collection <- collectionNames(object)[[1L]]
set <- geneSetNames(object = object, collection = collection)[[1L]]
plotGeneSet(
    object = object,
    collection = collection,
    contrast = contrast,
    set = set
)

acidgenomics/acidgsea documentation built on Oct. 5, 2023, 7:35 p.m.