Implement all basic recipes for rectangular trees

[cvigilv]

Decided to implement all the things I wish to have ASAP here. The list is:

• treeplot
• treescatter
• treelabel
• treecladelabel
• treearea
• treepie
• treecollapsed

Related issues

Related #9, #10.

Superseeds #13.

Checklist

• I am following the contributing guidelines
• Tests are passing
• Lint workflow is passing
• Docs were updated and workflow is passing

[cvigilv]

Here is an example using all the functions implemented to the moment:

using Revise
using CairoMakie, NewickTree
import Makie
using BasicTreePlots
using AbstractTrees

# Basic example
begin
    tree = ((:a, :b), (:c, (:d, :e)))

    fig = Figure()
    ax = Axis(fig[1, 1], xautolimitmargin=(0.1, 0.5))
    hidedecorations!(ax)
    hidespines!(ax)
    treearea!(ax, tree; addstroke=true, strokestyle=:dashdot, strokewidth=1.0, strokecolor=:magenta, padding=[0.0, 0.0])
    treearea!(ax, tree; node=(:c, (:d, :e)), color=:green, alpha=0.2, padding=[0.3, 0.3])
    treearea!(ax, tree; node=(:d, :e), color=:green, alpha=0.2)
    treearea!(ax, tree; node=(:a, :b), color=:red, alpha=0.2)
    treelabels!(ax, tree, usemaxdepth=true, tipannotations=Dict(:a => "A", :b => "B", :c => "C", :d => "D", :e => "E"))
    treescatter!(ax, tree)
    treecladelabel!(ax, tree, node=(:d, :e), color=:green, font=:bold, label="Super-Interesting-Clade", lineoffset=1.0)
    treecladelabel!(ax, tree, node=(:c, (:d, :e)), color=:lime, label="Clade", rotation=pi / 2, lineoffset=0.5, linestyle=:dash, linewidth=3, align=(:center, :top))
    treeplot!(ax, tree)
    fig
end

[cvigilv]

Current status

• treeplot*: draws tree, allows for diffent styling (stripped down old version)
• treelabels: draws labels for given node, accepts a Dict to map label to node
• treescatter*: add points into the nodes (same as Add TreeScatter Makie recipe #13)
• treecladelabel: add label to clade (based on ggtree's geom_cladelabel)
• treearea: highlight nodes using polygon (based on ggtree's geom_hilight)

Note: Functions suffixed with * already have their PolarAxis implementation done.

Note: I extracted the labeling functionality of treeplot, but it has a bug when plotting if the argument usemaxdepth to false. I'm currently looking into this.

[cvigilv]

I was thinking on renaming the functions to (1) shorten them and (2) make them more similar to ggtree. For example:

• treelabels => labelnode
• treescatter => treenodes
• treecladelabel => labelclade

Let me know what you think, I really like the ggtree convention but its to atomic for how this package is structured.

[cvigilv]

Not the most pretty, but getting there

[cvigilv]

Update: due to how the plotting works, the treecollapsed function has to accept an argument nodestocollapse in order to convert the node into a collapsed representation. I find this ugly, since intuitively I would collapse the leafs after plotting the original tree. What do you think is the best way to handle this?