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Draw an UpSet plot from a data frame of logical columns

Source: R/upset_plot.R
upset_plot.Rd

This is a minimalistic implementation of upset plots, as used to visualise our qc_loci_report. It is not intended to be a general-purpose upset plotting function, and it does not attempt to replicate all the features of specialised packages. It produces a three-panel UpSet plot assembled with patchwork:

  • Top panel - bar chart of intersection sizes, labelled.

  • Matrix panel - dot-and-line membership matrix with alternating row backgrounds for readability.

  • Left panel - horizontal bar chart of per-set totals.

Usage

upset_plot(
  df,
  sets = NULL,
  min_size = 1L,
  n_intersections = 40L,
  bar_colour = "#2166ac",
  dot_colour = "#2166ac",
  empty_colour = "#d9d9d9",
  set_bar_colour = "#4dac26",
  text_size = 11
)

Arguments

df

A data frame with logical set-membership columns.

sets

Character vector of column names to use as sets. Defaults to NULL, in which case all logical columns are used automatically. The order of sets controls the top-to-bottom row order in the matrix (first element appears at the top).

min_size

Integer. Intersections with fewer than this many rows are dropped. Default 1L.

n_intersections

Integer. Maximum number of intersections to display (top-n by count). Default 40L.

bar_colour

Fill colour for the intersection size bars. Default "#2166ac".

dot_colour

Colour for filled dots and connecting lines in the membership matrix. Default "#2166ac".

empty_colour

Colour for absent-set dots in the matrix. Default "#d9d9d9".

set_bar_colour

Fill colour for the set-size bars. Default "#4dac26".

text_size

Base font size (pts) passed to all theme calls. Default 11.

Value

A patchwork object. Print it or pass it to ggsave.

Examples

set.seed(1)
df <- data.frame(
  A = sample(c(TRUE, FALSE), 100, replace = TRUE),
  B = sample(c(TRUE, FALSE), 100, replace = TRUE),
  C = sample(c(TRUE, FALSE), 100, replace = TRUE)
)
upset_plot(df)