Heatmap

Heatmap

Usage

plotHeatmap(object, ...)

# S4 method for 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
)
#> Contrast: condition_B_vs_A
#> Factor column: condition
#> Numerator samples: "sample7", "sample8", "sample9", "sample10", "sample11"...
#> Denominator samples: "sample1", "sample2", "sample3", "sample4", "sample5"...
#> → Scaling matrix per row (z-score).
#> → Performing hierarchical clustering with `hclust()` method "ward.D2".