UpSet plot of directional enriched pathway intersections across contrasts — plotEnrichedUpset • AcidGSEA

UpSet plot of directional enriched pathway intersections across contrasts

Usage

plotEnrichedUpset(object, ...)

# S4 method for class 'FgseaList'
plotEnrichedUpset(object, collection, direction = c("both", "up", "down"))

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.
...: Additional arguments.

Value

Plot.

Note

Updated 2022-04-27.

Examples

data(fgsea)

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