agitated.Rd
A lightweight (and reasonably efficient) alternative to the UpSetR package. These plots allow visualisation of an arbitrary number of set interactions (see http://doi.org/gbjxr9).
agitated( x, nsets = 20, exclusive = TRUE, intersection_order = c("frequency", "degree"), sort_sets = TRUE, title = NULL, subtitle = NULL, return_plots = FALSE )
x | A list or presence/absence matrix. |
---|---|
nsets | Numeric scalar specifying the maximum number of sets to be shown. |
exclusive | Logical scalar controlling whether the intersections should be exclusive. |
intersection_order | Character scalar controlling whether sorting of
intersections is done by |
sort_sets | Logical scalar controlling whether the input sets are re-ordered based on descending size. |
title, subtitle | Character scalars specifying plot title and subtitle. |
return_plots | Logical scalar specifying whether the ggplot2 objects
should be returned directly ( |
If return_plots = TRUE
, the function returns a list of three
ggplot2 objects.
If return_plots = TRUE
,
the function calls plot_grid
on the plot objects.
agitated: produce an upset plot
UpSetR: an R package for the visualization of intersecting sets and their properties Jake R Conway, Alexander Lex, Nils Gehlenborg <doi:10.1093/bioinformatics/btx364>.
data <- agitated:::example_data() agitated(data)#> Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.agitated(data, nsets = 10)#> Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.agitated(data, exclusive = FALSE)#> Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.agitated(data, intersection_order = "degree")#> Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.agitated(data, sort_sets = FALSE)#> Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.agitated(data, title = "title", subtitle = "subtitle")#> Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.