treeplot

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.

Examples

Quick snippet for seeing basic features

using NewickTree, CairoMakie
tree = nw"((a:0.1, b:0.2):0.3, (c:0.5, (d:0.3, e:0.1):0.1):0.2);"
fig = Figure(size=(500, 500))
layoutstyles = (:dendrogram, :cladogram)
branchstyles = (:square, :straight)
for i in 1:2, j in 1:2
ax, tp = treeplot(fig[i,j], tree;
layoutstyle=layoutstyles[i],
branchstyle=branchstyles[j],
axis=(; title=join([layoutstyles[i]), ", ", branchstyles[j]])
)
treelabels!(tp.nodepoints)
scatter!(tp.orderedpoints)
end
fig

This can then be annotated with treehilight, treelabels, and treecladelabel plots

Plot type

The plot type alias for the treeplot function is TreePlot.

Attributes

alpha = 1.0 — The alpha value of the colormap or color attribute. Multiple alphas like in plot(alpha=0.2, color=(:red, 0.5), will get multiplied.

branchcolor = @inherit color :black — 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.

branchpointresolution = 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.

branchstyle = :square — Available options are :square or :straight. :square will display line from child to parent by 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 direct line from child to parent.

branchwidth = @inherit linewidth 1.0 — Can be either a single width of type Real or a vector of numbers for each node in pre-walk order. width for each node is associated to the branch connecting it to its parent.

clip_planes = @inherit clip_planes automatic — Clip planes offer a way to do clipping in 3D space. You can set a Vector of up to 8 Plane3f planes here, behind which plots will be clipped (i.e. become invisible). By default clip planes are inherited from the parent plot or scene. You can remove parent clip_planes by passing Plane3f[].

colormap = @inherit colormap :viridis — Sets the colormap that is sampled for numeric colors. PlotUtils.cgrad(...), Makie.Reverse(any_colormap) can be used as well, or any symbol from ColorBrewer or PlotUtils. To see all available color gradients, you can call Makie.available_gradients().

colorrange = automatic — The values representing the start and end points of colormap.

colorscale = identity — The color transform function. Can be any function, but only works well together with Colorbar for identity, log, log2, log10, sqrt, logit, Makie.pseudolog10, Makie.Symlog10, Makie.AsinhScale, Makie.SinhScale, Makie.LogScale, Makie.LuptonAsinhScale, and Makie.PowerScale.

depth_shift = 0.0 — Adjusts the depth value of a plot after all other transformations, i.e. in clip space, where -1 <= depth <= 1. This only applies to GLMakie and WGLMakie and can be used to adjust render order (like a tunable overdraw).

fxaa = true — Adjusts whether the plot is rendered with fxaa (fast approximate anti-aliasing, GLMakie only). Note that some plots implement a better native anti-aliasing solution (scatter, text, lines). For them fxaa = true generally lowers quality. Plots that show smoothly interpolated data (e.g. image, surface) may also degrade in quality as fxaa = true can cause blurring.

highclip = automatic — The color for any value above the colorrange.

inspectable = @inherit inspectable — Sets whether this plot should be seen by DataInspector. The default depends on the theme of the parent scene.

inspector_clear = automatic — Sets a callback function (inspector, plot) -> ... for cleaning up custom indicators in DataInspector.

inspector_hover = automatic — Sets a callback function (inspector, plot, index) -> ... which replaces the default show_data methods.

inspector_label = automatic — Sets a callback function (plot, index, position) -> string which replaces the default label generated by DataInspector.

layoutstyle = :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.

leafoffset = 0 — Offset added to first leaf. At default leaves start counting from 1. Set to -1 to start counting from 0. Useful for starting the first leaf pointing directly right when using PolarAxis or setting the first leaf at the y origin when using Axis

lowclip = automatic — The color for any value below the colorrange.

maxdepthoffset = 0.0 — No docs available.

model = automatic — Sets a model matrix for the plot. This overrides adjustments made with translate!, rotate! and scale!.

nan_color = :transparent — The color for NaN values.

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 leafoffset to 2π - openangle.

orientation = :right — Options are :right, :top, :left', and:bottom, and indicate where the leaves point away from the root.:rightand:topwill keep the root at zero the leaves will increase in distance on thexandyaxis respectively.:leftandbottomwill translate the tree after multiplying the axis by-1so that the deepest leaf is at0` and the internal nodes increase in height away from that leaf.

To keep the root at zero but the leaves pointing down, use orientation=:top in combination with Axis(figloc; yreversed=true).

overdraw = false — Controls if the plot will draw over other plots. This specifically means ignoring depth checks in GL backends

showroot = false — If BasicTreePlots.distance() is not nan for root, show line linking root to parent.

space = :data — Sets the transformation space for box encompassing the plot. See Makie.spaces() for possible inputs.

ssao = false — Adjusts whether the plot is rendered with ssao (screen space ambient occlusion). Note that this only makes sense in 3D plots and is only applicable with fxaa = true.

transformation = :automatic — Controls the inheritance or directly sets the transformations of a plot. Transformations include the transform function and model matrix as generated by translate!(...), scale!(...) and rotate!(...). They can be set directly by passing a Transformation() object or inherited from the parent plot or scene. Inheritance options include:

• :automatic: Inherit transformations if the parent and child space is compatible
• :inherit: Inherit transformations
• :inherit_model: Inherit only model transformations
• :inherit_transform_func: Inherit only the transform function
• :nothing: Inherit neither, fully disconnecting the child's transformations from the parent

Another option is to pass arguments to the transform!() function which then get applied to the plot. For example transformation = (:xz, 1.0) which rotates the xy plane to the xz plane and translates by 1.0. For this inheritance defaults to :automatic but can also be set through e.g. (:nothing, (:xz, 1.0)).

transparency = false — Adjusts how the plot deals with transparency. In GLMakie transparency = true results in using Order Independent Transparency.

usemaxdepth = false — If true draw lines of 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).

visible = true — Controls whether the plot gets rendered or not.