plot_upset {iCOBRA} | R Documentation

## Create UpSet plots

### Description

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

### Author(s)

Charlotte Soneson

### 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.

### Examples

    data(cobradata_example)
    cobraperf <- calculate_performance(cobradata_example,
                                       binary_truth = "status",
                                       aspects = "overlap")
    cobraplot <- prepare_data_for_plot(cobraperf, colorscheme = "Dark2",
                                       incltruth = TRUE)
    plot_upset(cobraplot)
    plot_upset(cobraplot, order.by = "freq", decreasing = TRUE)

    cobraperf <- calculate_performance(cobradata_example,
                                       binary_truth = "status",
                                       aspects = "overlap",
                                       splv = "expr_cat")
    cobraplot <- prepare_data_for_plot(cobraperf, colorscheme = "Dark2",
                                       incltruth = TRUE)
    plot_upset(cobraplot, stratum = "[2.85e+00,1.45e+01)")

[Package iCOBRA version 1.22.2 Index]