upset {ComplexUpset}

Compose an UpSet plot

Description

Compose an UpSet plot

Usage

upset(
  data,
  intersect,
  base_annotations = "auto",
  name = "group",
  annotations = list(),
  themes = upset_themes,
  stripes = upset_stripes(),
  labeller = identity,
  height_ratio = 0.5,
  width_ratio = 0.3,
  wrap = FALSE,
  set_sizes = upset_set_size(),
  mode = "distinct",
  queries = list(),
  guides = NULL,
  encode_sets = TRUE,
  matrix = intersection_matrix(),
  ...
)

Arguments

data

a dataframe including binary columns representing membership in classes

intersect

which columns should be used to compose the intersection

base_annotations

a named list with default annotations (i.e. the intersection size barplot)

name

the label shown below the intersection matrix

annotations

a named list of annotations, each being a list with: ⁠list(aes=mapping, geom=geom or list of geoms)⁠;

• (optional) ⁠highlight_geom=list of geoms⁠ geoms which can be highlighted with queries,

• (optional) ⁠top_geom=list of geoms⁠ which should show up on top of highlighted queries.

themes

a named list of themes for components and annotations, see upset_default_themes()/upset_modify_themes()

stripes

specification of the stripes appearance created with upset_stripes()

labeller

function modifying the names of the sets (rows in the matrix)

height_ratio

ratio of the intersection matrix to intersection size height

width_ratio

ratio of the overall set size width to intersection matrix width

wrap

whether the plot should be wrapped into a group (makes adding a tile/combining with other plots easier)

set_sizes

the overall set sizes plot, e.g. from upset_set_size() (FALSE to hide)

mode

region selection mode for computing the number of elements in intersection fragment. See get_size_mode() for accepted values.

queries

a list of queries generated with upset_query()

guides

action for legends aggregation and placement ('keep', 'collect', 'over' the set sizes)

encode_sets

whether set names (column in input data) should be encoded as numbers (set to TRUE to overcome R limitations of max 10 kB for variable names for datasets with huge numbers of sets); default TRUE for upset() and FALSE for upset_data().

matrix

the intersection matrix plot

...

Arguments passed on to upset_data

min_size

minimal number of observations in an intersection for it to be included

max_size

maximal number of observations in an intersection for it to be included

min_degree

minimal degree of an intersection for it to be included

max_degree

maximal degree of an intersection for it to be included

n_intersections

the exact number of the intersections to be displayed; n largest intersections that meet the size and degree criteria will be shown

keep_empty_groups

whether empty sets should be kept (including sets which are only empty after filtering by size)

warn_when_dropping_groups

whether a warning should be issued when empty sets are being removed

warn_when_converting

whether a warning should be issued when input is not boolean

sort_sets

whether to sort the rows in the intersection matrix (descending sort by default); one of: 'ascending', 'descending', FALSE

sort_intersections

whether to sort the columns in the intersection matrix (descending sort by default); one of: 'ascending', 'descending', FALSE

sort_intersections_by

the mode of sorting, the size of the intersection (cardinality) by default; one of: 'cardinality', 'degree', 'ratio', or any combination of these (e.g. c('degree', 'cardinality'))

sort_ratio_numerator

the mode for numerator when sorting by ratio

sort_ratio_denominator

the mode for denominator when sorting by ratio

group_by

the mode of grouping intersections; one of: 'degree', 'sets'

size_columns_suffix

suffix for the columns to store the sizes (adjust if conflicts with your data)

intersections

whether only the intersections present in data (observed, default), or all intersections (all) should be computed; using all intersections for a high number of sets is not computationally feasible - use min_degree and max_degree to narrow down the selection; this is only useful for modes different from the default exclusive intersection. You can also provide a list with a custom selection of intersections (order is respected when you set sort_intersections=FALSE)

max_combinations_datapoints_n

a fail-safe limit preventing accidental use of intersections='all' with a high number of sets and observations