[ANN] UpSetPlot.jl

[ljournot]

Announcing UpSetPlot.jl

I announce UpSetPlot.jl, a (minimalist) Julia package for plotting UpSet plots, a data visualization method for showing set data with more than three intersecting sets. UpSet plots are now frequently used instead of Venn diagrams, especially in life sciences.

Features

• Plots UpSet plots
• Horizontal, vertical, opt. cumulative intersection size for each intersection degree.
• Produces the lists of elements specific to each set intersections.

Installation

using Pkg
Pkg.add("UpSetPlot")

Example

julia> using UpSetPlot
julia> using DataFrames
julia> set_names = ["Set1", "Set2", "Set3", "Set4", "Set5", "Set6"]
julia> df1 = DataFrame(
    Set1 = ["ID01", "ID02", "ID03", "ID07", "ID08", "ID09", "ID10", "ID04", "ID05", "ID06"],
    Set2 = ["ID01", "ID02", "ID03", "ID04", "ID05", "ID11", "ID12", "ID13", "ID14", "ID15"],
    Set3 = ["ID01", "ID02", "ID03", "ID07", "ID13", missing, missing, missing, missing, missing],
    Set4 = ["ID16", "ID17", "ID18", "ID19", "ID14", "ID02", "ID03", missing, missing, missing],
    Set5 = fill(missing, 10),
    Set6 = ["ID01", "ID02", "ID03", "ID04", "ID05", "ID11", "ID12", "ID13", "ID16", missing],
    Col_x = ["x1", "x2", "x3", "x4", "x5", "x6", "x7", "x8", "x9", "x10"]
)
julia> df2 = DataFrame(
    id = ["ID01", "ID02", "ID03", "ID04", "ID05", "ID06", "ID07", "ID08", "ID09", "ID10", "ID11", "ID12", "ID13", "ID14", "ID15", "ID16", "ID17", "ID18", "ID19"],
    Set1 = [true, true, true, true, true, true, true, true, true, true, false, false, false, false, false, false, false, false, false],
    Set2 = [true, true, true, true, true, false, false, false, false, false, true, true, true, true, true, false, false, false, false],
    Set3 = [true, true, true, false, false, false, true, false, false, false, false, false, true, false, false, false, false, false, false],
    Set4 = [false, true, true, false, false, false, false, false, false, false, false, false, false, true, false, true, true, true, true],
    Set5 = fill(false, 19),
    Set6 = [true, true, true, true, true, false, false, false, false, false, true, true, true, false, false, true, false, false, false]
)
julia> fig1, lists1 = upset_plot(df1; set_names=set_names, intersection_lists=true);
julia> fig2, lists2 = upset_plot(df2; orientation=:h, cumul=true, intersection_lists=true);
julia> lists1 == lists2
true
julia> lists1["Set1"] == ["ID06", "ID08", "ID09", "ID10"]
true
julia> lists2["Set1_Set2_Set6"] == ["ID04", "ID05"]
true
julia> to_dataframe(lists1)

julia> display(fig1)

julia> display(fig2)