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Prepare UpSet co-occurrence data for plotting

Source: R/upset-plot.R
hv_upset.Rd

Validates a set-membership data frame, checks all intersect columns are binary (logical or 0/1 integer), computes per-set counts, and returns an hv_upset object. Call plot.hv_upset on the result to obtain a ggplot2 UpSet diagram (backed by scale_x_upset).

Usage

hv_upset(data, intersect)

Arguments

data

A data frame. Each set-membership column must be logical or integer (0/1).

intersect

Character vector of column names to treat as sets. Must contain at least two names that exist in data.

Value

An object of class c("hv_upset", "hv_data"):

$data

The validated input data frame, plus a .Procedures list-column derived from the indicator matrix (consumed by scale_x_upset()).

$meta

Named list: intersect, n_patients, n_sets.

$tables

List with one element: set_counts – a named integer vector of per-set patient counts.

See also

plot.hv_upset, sample_upset_data

Examples

sets <- c("AV_Replacement", "AV_Repair", "MV_Replacement", "MV_Repair",
          "TV_Repair", "Aorta", "CABG")
dta <- sample_upset_data(n = 300, seed = 42)

# 1. Build data object
up <- hv_upset(dta, intersect = sets)
up  # prints set counts
#> <hv_upset>
#>   N patients  : 300  (7 sets)
#>   Set counts  :
#>     AV_Replacement       93
#>     AV_Repair            40
#>     MV_Replacement       45
#>     MV_Repair            33
#>     TV_Repair            36
#>     Aorta                37
#>     CABG                 114

# 2. Plot. The default (set_size = TRUE) returns a patchwork composite,
# so apply themes with `&` to theme every sub-panel. Use `+` for
# set_size = FALSE (a plain ggplot).
plot(up) & theme_hv_poster()
#> Warning: Removed 30 rows containing non-finite outside the scale range (`stat_count()`).
#> Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
#> ℹ Please use `linewidth` instead.
#> ℹ The deprecated feature was likely used in the ggupset package.
#>   Please report the issue at <https://github.com/const-ae/ggupset/issues>.

plot(up, set_size = FALSE) + theme_hv_poster()
#> Warning: Removed 30 rows containing non-finite outside the scale range (`stat_count()`).