Compose an UpSet plot

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