plotLfc: Plot log2 fold change distributions

In acidgenomics/pfgsea: Acid Genomics GSEA

Plot log2 fold change distributions

Description

Plot log2 fold change distributions

Usage

plotLfc(object, ...)

## S4 method for signature 'FgseaList'
plotLfc(
  object,
  contrast = NULL,
  collection,
  set,
  geom = c("boxplot", "boxplot"),
  points = TRUE,
  labels = list(title = "log2 fold change", subtitle = NULL)
)

Arguments

object	Object.
contrast	character or NULL. Contrast name. If NULL, plot all contrasts.
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".
geom	character(1). Plot type. Uses match.arg() internally and defaults to the first argument in the character vector.
points	logical(1). Show individual data points.
labels	list. ggplot2 labels. See ggplot2::labs() for details.
...	Additional arguments.

Value

ggplot.

Note

Updated 2023-08-15.

Examples

data(fgsea)

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

acidgenomics/pfgsea documentation built on April 5, 2025, 9:18 a.m.