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Plot an hv_upset object

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

Draws an UpSet plot using upset. Apply a theme to all panels with &:

plot(up) & hv_theme("poster")

Apply scales or annotations to the intersection panel via base_annotations.

Usage

# S3 method for class 'hv_upset'
plot(
  x,
  min_size = 1,
  width_ratio = 0.3,
  encode_sets = FALSE,
  sort_sets = "descending",
  sort_intersections = "descending",
  set_size_position = "right",
  ...
)

Arguments

x

An hv_upset object.

min_size

Minimum intersection size to display. Default 1.

width_ratio

Fraction of horizontal space given to the set-size bar. Default 0.3.

encode_sets

Logical; when FALSE (default) set names are used verbatim, required for annotate to reference a specific set by name.

sort_sets

Sort order for set-size bar: "descending", "ascending", or FALSE. Default "descending".

sort_intersections

Sort order for intersection size bars. Default "descending".

set_size_position

Position of the set-size bar: "right" (default) or "left".

...

Additional arguments forwarded to upset, e.g. base_annotations, annotations, set_sizes.

Value

A patchwork / ggplot composite. Use & to apply a theme to all panels.

See also

hv_upset, hv_theme

Examples

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

# Build the plot object (render interactively with print(p))
p <- plot(up)
#> 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 ComplexUpset package.
#>   Please report the issue at
#>   <https://github.com/krassowski/complex-upset/issues>.
#> Warning: themes$intersections_matrix is not a valid theme.
#> Please use `theme()` to construct themes.
#> Warning: `legend.margin` must be specified using `margin()`
#> ℹ For the old behavior use `legend.spacing`
#> Warning: themes$intersections_matrix is not a valid theme.
#> Please use `theme()` to construct themes.
#> Warning: selected_theme is not a valid theme.
#> Please use `theme()` to construct themes.
#> Warning: `legend.margin` must be specified using `margin()`
#> ℹ For the old behavior use `legend.spacing`
#> Warning: selected_theme is not a valid theme.
#> Please use `theme()` to construct themes.
#> Warning: themes$overall_sizes is not a valid theme.
#> Please use `theme()` to construct themes.
#> Warning: `legend.margin` must be specified using `margin()`
#> ℹ For the old behavior use `legend.spacing`
#> Warning: themes$overall_sizes is not a valid theme.
#> Please use `theme()` to construct themes.

if (FALSE) { # \dontrun{
# Manuscript theme applied to all panels via &
plot(up) & hv_theme("poster")

# Custom intersection bar colour
plot(up,
  base_annotations = list(
    "Intersection size" = ComplexUpset::intersection_size(
      mapping = ggplot2::aes(fill = "n")
    ) +
      ggplot2::scale_fill_manual(
        values = c("n" = "steelblue"),
        guide  = "none"
      ) +
      ggplot2::labs(y = "Patients (n)")
  )
) &
  hv_theme("poster")
} # }