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Plot log2 fold change distributions

Usage

plotLfc(object, ...)

# S4 method for 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
)