Add TreeScatter Makie recipe

docs/src/literate-gallery/big_phylogeny.jl

@@ -0,0 +1,37 @@
+using CairoMakie, NewickTree, BasicTreePlots, AbstractTrees
+
+tree =
+    nw"((6669.DappuP312785:1.24473,(((7739.JGI126010:4.02e-06,7739.JGI126021:0.168081)0.99985:0.848895,((45351.NEMVEDRAFT_v1g217973-PA:1.49614,(6085.XP_002167371:1.08059,10228.TriadP54105:1.08509)0.457684:0.128729)0.99985:0.321915,(7668.SPU_016633tr:0.00222941,7668.SPU_013365tr:0.093091)0.99985:0.642533)0.888302:0.101463)0.998565:0.12537,((51511.ENSCSAVP00000011400:0.259936,7719.ENSCINP00000035803:0.209259)0.99985:1.762,(7757.ENSPMAP00000006833:0.945887,((7955.ENSDARP00000103018:0.187989,(8049.ENSGMOP00000003903:0.283082,((8128.ENSONIP00000009923:0.172432,(69293.ENSGACP00000005927:0.11289,(99883.ENSTNIP00000008530:0.0637802,31033.ENSTRUP00000029741:0.0851327)0.99985:0.111539)0.750558:0.0140823)0.99985:0.0210439,(8083.ENSXMAP00000007211:0.156672,8090.ENSORLP00000021771:0.242897)0.99985:0.0332475)0.99985:0.0502247)0.99985:0.097906)0.99985:0.204816,(7897.ENSLACP00000021045:0.20103,(8364.ENSXETP00000053091:0.389689,((9258.ENSOANP00000015194:0.652603,((13616.ENSMODP00000032296:0.0669026,(9315.ENSMEUP00000005072:0.0368095,9305.ENSSHAP00000018667:0.0280404)0.997706:0.0140274)0.99985:0.109803,((9361.ENSDNOP00000011178:0.093465,(9371.ENSETEP00000005953:0.276816,(9813.ENSPCAP00000009886:0.0800451,9785.ENSLAFP00000023898:0.0550027)0.99697:0.0294647)0.99985:0.0375967)0.608183:0.00574174,((((30608.ENSMICP00000006810:0.0353003,30611.ENSOGAP00000013460:0.0515798)0.99985:0.034051,(9478.ENSTSYP00000011163:0.0656837,(9483.ENSCJAP00000037059:0.0556713,(9544.ENSMMUP00000001688:0.00821597,(61853.ENSNLEP00000001585:0.00543935,(9601.ENSPPYP00000009641:0.00544861,(9593.ENSGGOP00000014253:0.00241737,(9606.ENSP00000299886:0.00108745,9598.ENSPTRP00000016297:0.00216932)0.993995:0.00108247)0.99985:0.00217395)0.99985:0.00216928)0.99985:0.00380297)0.99985:0.00880979)0.99985:0.0259329)0.993631:0.00725957)0.99985:0.00775695,((((10141.ENSCPOP00000018381:0.0312261,10141.ENSCPOP00000003239:0.0560276)0.99985:0.131426,(10090.ENSMUSP00000018805:0.0326181,10116.ENSRNOP00000003804:0.0330137)0.99985:0.081468)0.995671:0.0105266,(43179.ENSSTOP00000001636:0.0584822,10020.ENSDORP00000002346:0.148367)0.976029:0.00712029)0.99985:0.020967,(9986.ENSOCUP00000010215:0.342444,37347.ENSTBEP00000010812:0.0710806)0.981559:0.0148504)0.99985:0.0111655)0.99985:0.0141806,((9823.ENSSSCP00000018275:0.0497089,(9739.ENSTTRP00000004916:0.0624029,9913.ENSBTAP00000007999:0.0933538)0.99985:0.0153799)0.99985:0.0353429,((9796.ENSECAP00000006507:0.0593149,(9685.ENSFCAP00000004377:0.0895056,(9615.ENSCAFP00000006718:0.0344248,(9646.ENSAMEP00000002816:0.0246918,9669.ENSMPUP00000014182:0.157245)0.979337:0.0106908)0.990824:0.00781435)0.99985:0.0209773)0.99291:0.00461526,(59463.ENSMLUP00000015199:0.175449,132908.ENSPVAP00000006353:0.0636063)0.828177:0.00861023)0.805512:0.00313751)0.99985:0.0138134)0.99985:0.0180555)0.99985:0.0925821)0.99985:0.0504324)0.99985:0.0408666,(28377.ENSACAP00000014302:0.2972,(13735.ENSPSIP00000020553:0.125656,(59729.ENSTGUP00000002997:0.21101,(9103.ENSMGAP00000006649:0.034221,9031.ENSGALP00000007041:0.0301602)0.99985:0.14558)0.99985:0.0950631)0.912514:0.0193477)0.99985:0.0543705)0.99985:0.0558399)0.99985:0.0851946)0.996306:0.0767894)0.99985:0.242292)0.99843:0.214734)0.760404:0.170331)0.99985:0.889243)0.99985:0.309174,((7070.TC009561-PA:1.414,(7029.ACYPI001869-PA:2.67503,((34740.HMEL012959-PA:0.216556,(13037.EHJ66433:0.30242,7091.BGIBMGA012450-TA:0.234676)0.691542:0.0356537)0.99985:1.06833,(7425.NV10250-PA:0.448078,(7460.GB18353-PA:0.265179,12957.ACEP_00009457-PA:0.219522)0.99985:0.223062)0.99985:0.715703)0.950323:0.0960579)0.630765:0.0828761)0.868488:0.104171,(121225.PHUM413450-PA:1.38201,(((43151.ADAR004533-PA:0.286189,7165.AGAP001322-PA:0.216522)0.99985:0.404262,(7176.CPIJ007948-PA:0.310705,7159.AAEL007141-PA:0.261808)0.99985:0.238196)0.99985:0.352684,(7260.FBpp0240708:0.24283,((7222.FBpp0149372:0.191481,7244.FBpp0224481:0.114954)0.99985:0.156407,(7237.FBpp0281462:0.118908,(7217.FBpp0120932:0.132407,(7245.FBpp0269552:0.0320153,7227.FBpp0082093:0.0340969)0.99985:0.0854297)0.99985:0.0800303)0.99985:0.0655239)0.825983:0.0710402)0.99985:1.14395)0.99985:0.708932)0.628915:0.0819834)0.99985:0.309174);"
+
+fig = Figure(size = (500, 500))
+ax = PolarAxis(fig[1, 1]; rautolimitmargin = (0.05, 0.1))
+
+c = map(PreOrderDFS(tree)) do node
+    BasicTreePlots.leafcount(node)
+end
+
+treeplot
+treeplot!(
+    ax,
+    tree,
+    layoutstyle = :cladogram,
+    branchstyle = :straight,
+    ignorebranchlength = true,
+    tipannotationsvisible = true,
+    usemaxdepth = true,
+    linecolor = :gainsboro,
+)
+s = treescatter!(
+    ax,
+    tree,
+    layoutstyle = :cladogram,
+    branchstyle = :straight,
+    ignorebranchlength = true,
+    markercolor = log2.(c),
+    colormap = :inferno,
+    alpha = 0.5,
+)
+hidedecorations!(ax)
+hidespines!(ax)
+Colorbar(fig[1, 2][3, 1], s, label = "# leafs (log2)")
+fig

docs/src/literate-gallery/phylogeny_of_organisms.jl

@@ -0,0 +1,54 @@
+# # Phylogeny of some organisms
+using CairoMakie, NewickTree, AbstractTrees, BasicTreePlots
+
+tree =
+    nw"(Bovine:0.69395,(Gibbon:0.36079,(Orangutan:0.33636,(Gorilla:0.17147,(Chimp:0.19268,Human:0.11927):0.08386):0.06124):0.15057):0.54939,Mouse:1.21460);"
+
+isprimate = Dict(
+    "Bovine" => false,
+    "Gibbon" => true,
+    "Orangutan" => true,
+    "Gorilla" => true,
+    "Chimp" => true,
+    "Human" => true,
+    "Mouse" => false,
+)
+tree_data = Dict(
+    node => (;
+        is_primate = get(isprimate, nodevalue(node).data.name, missing),
+        bananas_ate = 25 * rand(),
+    ) for node in PreOrderDFS(tree)
+)
+
+markercolors = map(PreOrderDFS(tree)) do node
+    if haskey(isprimate, nodevalue(node).data.name)
+        if tree_data[node].is_primate
+            :gold
+        else
+            :black
+        end
+    else
+        :transparent
+    end
+end
+
+markersizes = map(PreOrderDFS(tree)) do node
+    if haskey(isprimate, nodevalue(node).data.name)
+        if isprimate[nodevalue(node).data.name]
+            1 + tree_data[node].bananas_ate * 2.0
+        else
+            1 + tree_data[node].bananas_ate * 0.5
+        end
+    else
+        0
+    end
+end
+
+
+fig = Figure()
+ax = Axis(fig[1, 1], xautolimitmargin = (0.0, 0.2))
+hidedecorations!(ax)
+hidespines!(ax)
+treeplot!(ax, tree, usemaxdepth = true)
+treescatter!(ax, tree, markercolor = markercolors, markersize = markersizes)
+fig

docs/src/literate-tutorials/basics.jl

@@ -76,6 +76,16 @@ hidespines!(ax)
 treeplot!(tree; linecolor = branchcolors, tipfontsize = 12)
 fig
 
+# or employ markers in the nodes to showcase the tree's information
+
+fig = Figure()
+ax = PolarAxis(fig[1, 1], rautolimitmargin = (0.0, 0.1))
+hidedecorations!(ax)
+hidespines!(ax)
+treeplot!(tree; tipfontsize = 12)
+treescatter!(tree; markercolor = branchcolors)
+fig
+
 # For instance if we have external data about each node in the tree
 
 tree_data = Dict(

ext/BasicTreePlotsMakieExt.jl

@@ -1,11 +1,14 @@
 module BasicTreePlotsMakieExt
 
 import BasicTreePlots
-import BasicTreePlots: treeplot, treeplot!
+import BasicTreePlots: treeplot, treeplot!, treescatter, treescatter!
 
 import Makie
 import Makie: Point2f
 
+import AbstractTrees
+import AbstractTrees: PreOrderDFS
+
 Makie.@recipe(TreePlot, tree) do scene
     attr = Makie.Attributes(
         showroot = false,
@@ -17,10 +20,6 @@ Makie.@recipe(TreePlot, tree) do scene
         linewidth = @something(Makie.theme(scene, :linewidth), 1),
         linecolormap = @something(Makie.theme(scene, :colormap), :viridis),
         branch_point_resolution = 25,
-        markervisible = false,
-        markercolor = @something(Makie.theme(scene, :color), :black),
-        markersize = @something(Makie.theme(scene, :markersize), 5),
-        markercolormap = @something(Makie.theme(scene, :colormap), :viridis),
         usemaxdepth = false,
         tipannotationsvisible = true,
         tipannotations = nothing,
@@ -143,6 +142,49 @@ function Makie.plot!(plt::TreePlot)
     end
 end
 
+Makie.@recipe(TreeScatter, tree) do scene
+    attr = Makie.Attributes(
+        alpha = @something(Makie.theme(scene, :alpha), 1.0),
+        showroot = false,
+        layoutstyle = :dendrogram,
+        marker = @something(Makie.theme(scene, :marker), :circle),
+        markercolor = @something(Makie.theme(scene, :color), :black),
+        markersize = @something(Makie.theme(scene, :markersize), 5),
+        nodeordering = AbstractTrees.PreOrderDFS,
+        openangle = 0,
+    )
+    Makie.MakieCore.generic_plot_attributes!(attr)
+    return Makie.MakieCore.colormap_attributes!(attr, Makie.theme(scene, :colormap))
+end
+
+function Makie.plot!(plt::TreeScatter)
+    nleaves = BasicTreePlots.leafcount(plt.tree[])
+    toangle(y) = (y / (nleaves)) * (2π - (plt.openangle[] % 2pi))
+
+    ## Setup tree layout
+    nodecoords = BasicTreePlots.nodepositions(
+        plt.tree[];
+        showroot = plt.showroot[],
+        layoutstyle = plt.layoutstyle[],
+    )
+
+    ## Transform coordinate if plotting in Polar Axis
+    if occursin("Polar", string(plt.transformation.transform_func[]))
+        nodecoords = Dict(node => (toangle(y), x) for (node, (x, y)) in nodecoords)
+    end
+
+    ## Add markers in nodes
+    Makie.scatter!(
+        plt,
+        [nodecoords[node] for node in plt.nodeordering[](plt.tree[])],
+        alpha = plt.alpha[],
+        marker = plt.marker[],
+        markersize = plt.markersize[],
+        color = plt.markercolor[],
+        colormap = plt.colormap[];
+    )
+end
+
 theme_empty() = Makie.Theme(
     Axis = (;
         topspinevisible = false,

src/BasicTreePlots.jl

@@ -8,7 +8,7 @@ using AbstractTrees: nodevalue, children, PreOrderDFS
 const LAYOUTS = (:dendrogram, :cladogram, :radial)
 const BRANCHTYPES = (:square, :straight)
 
-export treeplot, treeplot!
+export treeplot, treeplot!, treescatter, treescatter!
 
 """
     treeplot(tree; kwargs...)
@@ -68,6 +68,43 @@ export treeplot, treeplot!
 function treeplot end
 function treeplot! end
 
+
+"""
+    treescatter(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:
+
+- `alpha::AbstractFloat = 1.0`, the alpha value of the colormap or color attribute. Multiple alphas like in `treescatter(alpha=0.2, color=(:red, 0.5))`, will get multiplied.
+
+- `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`.
+
+- `marker::Symbol = :circle`, sets the scatter marker shape.
+
+- `markercolor = :black`, sets the scatter marker color.
+
+- `markersize = 5`, sets the scatter marker size.
+
+- `nodeordering = AbstractTrees.PreOrderDFS`, function that informs algorithm which is the ordering of attributes
+    `marker`, `markercolor`, and `markersize`.
+
+- `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)`.
+
+
+"""
+function treescatter end
+function treescatter! end
+
 # public distance, label
 
 """