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Plot gene set enrichment

Source: R/AllGenerics.R, R/plotGeneSet-methods.R
plotGeneSet.Rd

Plot gene set enrichment

Usage

plotGeneSet(object, ...)

# S4 method for 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
)