plotEnrichedGeneSets: Plot enriched gene sets

In steinbaugh/pfgsea: Acid Genomics GSEA

Plot enriched gene sets

Description

Plot enriched gene sets

Usage

plotEnrichedGeneSets(object, ...)

## S4 method for signature 'FgseaList'
plotEnrichedGeneSets(
  object,
  collection,
  direction = c("both", "up", "down"),
  n = 10L,
  headerLevel = 3L
)

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.
direction	character(1). Include "both", "up", or "down" directions.
n	integer(1). Number to include.
headerLevel	integer(1) (1-7). Markdown header level.
...	Additional arguments.

Value

ggplot.

Note

Updated 2022-04-27.

See Also

plotGeneSet().

Examples

data(fgsea)

## FgseaList ====
object <- fgsea
alphaThreshold(object) <- 0.9
collection <- collectionNames(object)[[1L]]
plotEnrichedGeneSets(
    object = object,
    collection = collection,
    n = 1L
)

steinbaugh/pfgsea documentation built on Oct. 17, 2023, 11:24 a.m.