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BasicTreePlots

Documentation for BasicTreePlots.

This is a package that aims to provide generic plotting recipes for tree like data structures. As such the recipes should only require that your data structure fulfills the AbstractTrees interface, i.e. has AbstractTrees.children(YourType) defined.

Optionally, BasicTreePlots.distance(YourType) and BasicTreePlots.label(YourType) can be defined to allow plotting trees with variable distances between children and parent nodes and pretty printing of each node in the tree respectively.

Currently, we only provide Makie.jl backends, but are interested in contributions for recipes for Plots.jl and TidyPlots.jl. As well as any other backends or custom tree structures that don't work automatically. See the ext folder for example extensions.

Installation

using Pkg
Pkg.add("BasicTreePlots")

Or the development version with

using Pkg
Pkg.add("https://github.com/BenjaminDoran/BasicTreePlots.jl.git")

Basic usage

using CairoMakie, BasicTreePlots
tree = ((:a, :b), (:c, :d))
treeplot(tree)

see Tutorials and Gallery for more in depth examples

treeplot() documentation

see reference for other function's documentation

BasicTreePlots.treeplot — Function
treeplot(tree; kwargs...)

Args:

  • tree, the root node of a tree that has AbstractTrees.children() defined. All nodes should be reachable by using AbstractTrees.PreOrderDFS() iterator.

Keyword arguments:

  • showroot::Bool = false, if BasicTreePlots.distance() is not nan for root, show line linking root to parent.

  • layoutstyle::Symbol = :dendrogram available options are :dendrogram, or :cladogram

    • :dendrogram displays tree taking into account the distance between parent and children nodes as calculated from BasicTreePlots.distance(node). If the distance is not defined, it defaults to 1 and is equivalent to the :cladogram layout
    • :cladogram displays the tree where each distance from a child node to their parent is set to 1.

  • branchstyle::Symbol = :square available options are :square or :straight

    • :square will display line from child to parent as going back to the height of the parent, before connecting back to the parent node at a right angle.
    • straight will display line from child to parent as a straight line from child to parent.

  • linecolor = :black, should match the color option in Makie's lines plot. Can be either a single color :black, color plus alpha transperency (:black, 0.5), or a vector of numbers for each node in pre-walk order. color for each node is associated to the line connecting it to its parent.

  • linewidth = 1, should match the linewidth option in Makie's lines plot. Can be either a single width or a vector of numbers for each node in pre-walk order. width for each node is associated to the line connecting it to its parent.

  • linecolormap=:viridis color map associated to linecolor. can be symbel of known colormap or gradient created from cgrad(). see Makie's color documentation

  • branch_point_resolution = 25, number of points associated to each line segment. Can be decreased to increase plotting speed. Or, increased if lines that should be smooth are not.

  • usemaxdepth = false, if true draw guide lines from each leaf tip to the depth of the leaf that is maximally distant from root. Useful for connecting leaves to there location on the y axis (or θ axis if plotted on PolarAxis).

  • tipannotationsvisible::Bool = true, whether to show text labels for each leaf tip.

  • tipfontsize = 9.0f0, font size that tip labels are displayed at.

  • openangle = 0, Angle in radians that limits span of tree around the circle when plotted on PolarAxis. if openangle = deg2rad(5) then leaf tips will spread across angles 0 to (2π - openangle).

  • tipalign = (:left, :center) text alignment of tip labels. see Makie options

  • tipannotationoffset = (3.0f0, 0.0f0) offset of tip label from actual tip position. The first value is associated with the x axis, and the second is associated with the y axis. (Currently, only available for cartisian axis)

source

Contributors