upset: Compose an UpSet plot
In ComplexUpset: Create Complex UpSet Plots Using 'ggplot2' Components

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(),
  ...
)

`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