upset_data {ComplexUpset} R Documentation

Prepare data for UpSet plots

Description

Prepare data for UpSet plots

Usage

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"
)


Arguments

 data a dataframe including binary columns representing membership in classes intersect which columns should be used to compose the intersection 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' mode region selection mode for sorting and trimming by size. See get_size_mode() for accepted values. size_columns_suffix suffix for the columns to store the sizes (adjust if conflicts with your data) 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() max_combinations_datapoints_n a fail-safe limit preventing accidental use of intersections='all' with a high number of sets and observations 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)

[Package ComplexUpset version 1.3.3 Index]