Make an UpSet-style set intersection plot with plot_ly()

A reimplementation of the upset tool of Lex, Gehlenborg et al: a bar chart of set sizes, a bar chart of intersection sizes, and a grid showing which sets make up each intersection - drawn with plotly rather than base graphics so it stays interactive outside of a fixed set count, and so all elements of a given intersection can be plotted (rather than assigning every item to its highest-order intersection).

Usage

interactive_upset(
  sets,
  nintersects = 20,
  minorder = 1,
  set_sort = TRUE,
  bar_numbers = FALSE,
  show_empty_intersections = TRUE,
  intersection_assignment_type = c("upset", "all")
)

Arguments

sets

A named list of character vectors, one per set (e.g. up/down differential gene sets per contrast)

nintersects

Maximum number of intersections to display, ordered by size

minorder

Minimum number of sets that must be involved in an intersection for it to be shown

set_sort

Sort sets by size (ascending) before plotting?

bar_numbers

Add value labels above the intersection size bars?

show_empty_intersections

Include intersections/set combinations with zero members?

intersection_assignment_type

'upset' assigns each member to its highest-order intersection only (as in the original UpSet); 'all' counts a member in every intersection it belongs to

Value

output A plotly htmlwidget

References

Lex and Gehlenborg (2014). Points of view: Sets and intersections. <em>Nature Methods</em> 11, 779 (2014). http://www.nature.com/nmeth/journal/v11/n8/abs/nmeth.3033.html

Gehlenborg N (2016). <em>UpSetR: A More Scalable Alternative to Venn and Euler Diagrams for Visualizing Intersecting Sets</em>. R package version 1.3.0, https://CRAN.R-project.org/package=UpSetR

Examples

sets <- list(a = paste0("gene", 1:6), b = paste0("gene", 4:10), c = paste0("gene", 8:12))
interactive_upset(sets)
#> Warning: Ignoring 13 observations