plot_upset: Create UpSet plots

In markrobinsonuzh/iCOBRA: Comparison and Visualization of Ranking and Assignment Methods

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)")

markrobinsonuzh/iCOBRA documentation built on March 28, 2024, 2:01 p.m.