upset {ComplexUpset} R Documentation

## 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_sizeminimal number of observations in an intersection for it to be included max_sizemaximal number of observations in an intersection for it to be included min_degreeminimal degree of an intersection for it to be included max_degreemaximal degree of an intersection for it to be included n_intersectionsthe exact number of the intersections to be displayed; n largest intersections that meet the size and degree criteria will be shown keep_empty_groupswhether empty sets should be kept (including sets which are only empty after filtering by size) warn_when_dropping_groupswhether a warning should be issued when empty sets are being removed warn_when_convertingwhether a warning should be issued when input is not boolean sort_setswhether to sort the rows in the intersection matrix (descending sort by default); one of: 'ascending', 'descending', FALSE sort_intersectionswhether to sort the columns in the intersection matrix (descending sort by default); one of: 'ascending', 'descending', FALSE sort_intersections_bythe 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_numeratorthe mode for numerator when sorting by ratio sort_ratio_denominatorthe mode for denominator when sorting by ratio group_bythe mode of grouping intersections; one of: 'degree', 'sets' size_columns_suffixsuffix for the columns to store the sizes (adjust if conflicts with your data) intersectionswhether 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_na fail-safe limit preventing accidental use of intersections='all' with a high number of sets and observations

[Package ComplexUpset version 1.3.3 Index]