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Create UpSet plots

Source: R/plot_methods.R
plot_upset.Rd

Generate UpSet plots showing the overlaps among sets of significant feature for a given adjusted p-value threshold (see thr_venn argument of calculate_performance). Optionally, the truth can be included as a "perfect" method. Note that if the results are stratified, only one category at a time can be displayed.

Usage

plot_upset(
  cobraplot,
  stratum = NULL,
  nsets = NULL,
  nintersects = NULL,
  sets.bar.color = NULL,
  ...
)

Arguments

cobraplot

A COBRAPlot object.

stratum

If results are stratified, the category to plot results for. Can be numeric or categorical (the name of the category).

nsets

The number of methods to include. By default, it is determined automatically from the cobraplot object.

nintersects

The number of set intersections to display. By default, it is determined automatically from the cobraplot object.

sets.bar.color

The colors to use for the bars in the UpSet plot. By default, they are extracted from the plotcolors slot of the cobraplot object.

...

Additional arguments to UpSetR::upset.

Value

Nothing, displays a graph

References

Lex and Gehlenborg (2014): Points of view: Sets and intersections. Nature Methods 11, 779.

Lex et al (2014): UpSet: Visualization of intersecting sets. IEEE Transactions on Visualization and Computer Graphics 20(12), 1983-1992.

Author

Charlotte Soneson

Examples

data(cobradata_example)
cobraperf <- calculate_performance(cobradata_example,
                                   binary_truth = "status",
                                   aspects = "overlap")
#> Warning: Object doesn't have a slot sval. Please run update_cobradata(). For consistency, I will return an empty data.frame
cobraplot <- prepare_data_for_plot(cobraperf, colorscheme = "Dark2",
                                   incltruth = TRUE)
plot_upset(cobraplot)
#> Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
#> ℹ Please use tidy evaluation idioms with `aes()`.
#> ℹ See also `vignette("ggplot2-in-packages")` for more information.
#> ℹ The deprecated feature was likely used in the UpSetR package.
#>   Please report the issue to the authors.
#> 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 UpSetR package.
#>   Please report the issue to the authors.
#> Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
#> ℹ Please use the `linewidth` argument instead.
#> ℹ The deprecated feature was likely used in the UpSetR package.
#>   Please report the issue to the authors.

plot_upset(cobraplot, order.by = "freq", decreasing = TRUE)


cobraperf <- calculate_performance(cobradata_example, 
                                   binary_truth = "status", 
                                   aspects = "overlap",
                                   splv = "expr_cat")
#> Warning: Object doesn't have a slot sval. Please run update_cobradata(). For consistency, I will return an empty data.frame
cobraplot <- prepare_data_for_plot(cobraperf, colorscheme = "Dark2", 
                                   incltruth = TRUE)
plot_upset(cobraplot, stratum = "[2.85e+00,1.45e+01)")