Prepare data for UpSet plots
upset_data(
data,
intersect,
min_size = 0,
max_size = Inf,
min_degree = 0,
max_degree = Inf,
n_intersections = NULL,
keep_empty_groups = FALSE,
warn_when_dropping_groups = FALSE,
warn_when_converting = "auto",
sort_sets = "descending",
sort_intersections = "descending",
sort_intersections_by = "cardinality",
sort_ratio_numerator = "exclusive_intersection",
sort_ratio_denominator = "inclusive_union",
group_by = "degree",
mode = "exclusive_intersection",
size_columns_suffix = "_size",
encode_sets = FALSE,
max_combinations_datapoints_n = 10^10,
intersections = "observed"
)a dataframe including binary columns representing membership in classes
which columns should be used to compose the intersection
minimal number of observations in an intersection for it to be included
maximal number of observations in an intersection for it to be included
minimal degree of an intersection for it to be included
maximal degree of an intersection for it to be included
the exact number of the intersections to be displayed; n largest intersections that meet the size and degree criteria will be shown
whether empty sets should be kept (including sets which are only empty after filtering by size)
whether a warning should be issued when empty sets are being removed
whether a warning should be issued when input is not boolean
whether to sort the rows in the intersection matrix (descending sort by default); one of: 'ascending', 'descending', FALSE
whether to sort the columns in the intersection matrix (descending sort by default); one of: 'ascending', 'descending', FALSE
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'))
the mode for numerator when sorting by ratio
the mode for denominator when sorting by ratio
the mode of grouping intersections; one of: 'degree', 'sets'
region selection mode for sorting and trimming by size. See get_size_mode() for accepted values.
suffix for the columns to store the sizes (adjust if conflicts with your data)
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()
a fail-safe limit preventing accidental use of intersections='all' with a high number of sets and observations
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)