UpSet plot for peak category overlaps

Creates an UpSetR::upset() plot from a peak data frame containing logical has_overlap_* columns produced by repeated calls to find_overlap_peaks(). Any column matching has_overlap_ is automatically detected if sets is NULL.

Usage

upset_peaks(
  object,
  sets = NULL,
  set_labels = NULL,
  order_by = "freq",
  set_colors = c("#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628"),
  title = NULL,
  output_pdf = NULL,
  width = 12,
  height = 8
)

Arguments

object

A data.frame with logical columns named has_overlap_*.

sets

Character vector. Column names to include. If NULL (default), all has_overlap_* columns are used automatically.

set_labels

Character vector. Display labels for each set. If NULL, labels are derived by removing the has_overlap_ prefix.

order_by

Character. "freq" (default) or "degree".

set_colors

Character vector. Bar colours for each set.

title

Character. Optional title above the plot. Default NULL.

output_pdf

Character. Optional path to save PDF. Default NULL.

width

Numeric. Plot width in inches. Default 12.

height

Numeric. Plot height in inches. Default 8.

Value

Invisibly returns the UpSet plot object.

Examples

if (FALSE) { # \dontrun{
data(example_peaks)
example_peaks$has_overlap_promoter <- sample(c(TRUE, FALSE),
                                             nrow(example_peaks),
                                             replace = TRUE)
example_peaks$has_overlap_enhancer <- sample(c(TRUE, FALSE),
                                             nrow(example_peaks),
                                             replace = TRUE)
upset_peaks(example_peaks, title = "Peak category overlaps")
} # }