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Plot normalized enrichment score

Source: R/AllGenerics.R, R/plotNes-methods.R
plotNes.Rd

Plot normalized enrichment score

Usage

plotNes(object, ...)

# S4 method for class 'FgseaList'
plotNes(
  object,
  contrast,
  collection,
  n = Inf,
  flip = getOption(x = "acid.flip", default = TRUE),
  labels = list(title = TRUE, subtitle = TRUE)
)

Arguments

object

Object.

contrast

character(1). Contrast name.

collection

character(1). Gene set collection name. Typically refers to h (hallmark), c1-c7 collections from MSigDb. Can obtain using collectionNames() on FgseaList object.

n

integer(1) or Inf. Number of gene sets (regardless of direction) to include in plot.

flip

logical(1). Flip x and y axes. Recommended for plots containing many samples.

labels

list. ggplot2 labels. See ggplot2::labs() for details.

...

Additional arguments.

Value

ggplot.

Details

Only plots gene sets that pass adjusted P value cutoff, defined by alphaThreshold.

Note

Updated 2023-08-15.

See also

Inspired by example in Stephen Turner's DESeq to fgsea guide.

Examples

data(fgsea)

## FgseaList ====
object <- fgsea
alphaThreshold(object) <- 0.9
contrast <- contrastNames(object)[[1L]]
collection <- collectionNames(object)[[1L]]
plotNes(
    object = object,
    contrast = contrast,
    collection = collection,
    n = 10L
)