plotHeatmap: Heatmap

In steinbaugh/pfgsea: Acid Genomics GSEA

Heatmap

Description

Heatmap

Usage

plotHeatmap(object, ...)

## S4 method for signature 'FgseaList'
plotHeatmap(
  object,
  contrast,
  contrastSamples = TRUE,
  collection,
  set,
  leadingEdge = FALSE,
  ...
)

Arguments

object	Object.
contrast	character(1). Contrast name.
contrastSamples	logical(1). Only visualize the samples defined in the contrast.
collection	character(1). Gene set collection name. Typically refers to h (hallmark), c1-c7 collections from MSigDb. Can obtain using collectionNames() on FgseaList object.
set	character(1). Gene set name, in a defined collection. For example, "HALLMARK_ADIPOGENESIS".
leadingEdge	logical(1). Visualize only the leading edge genes returned by GSEA. If FALSE, plot all genes in the gene set.
...	Additional arguments.

Value

Plot.

Note

Updated 2021-03-16.

Examples

data(fgsea)

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

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