Colour a tree by topology

PaintTree() assigns a colour to every edge, leaf, and internal node of a tree such that sister clades occupy adjacent hue bands proportional to their tip counts, and saturation grows from zero at the root to one at every tip. The result is a list of vectors that correspond to plot.phylo()'s edge.color, tip.color, and node.color arguments.

Usage

PaintTree(tree, palette = "default")

Arguments

tree

A tree of class phylo.

palette

Either a character string naming one of the built-in palettes ("default", "protanopia", "tritanopia", or a function function(h, s) taking vectors of hues in [0, 360] and saturations in [0, 1] and returning a character vector of colours. The "protanopia" and "tritanopia" palettes simulate dichromatic perception of the default HCL spectrum using the Viénot–Brettel–Mollon projection.

Value

A list with three character vectors of hex colours:

edgeCol

One colour per edge in tree$edge, taken from the child node's (hue, saturation).

tipCol

One colour per leaf, indexed 1:NTip(tree).

nodeCol

One colour per internal node, indexed so that entry i corresponds to node NTip(tree) + i; the root (entry 1) is grey because its saturation is zero.

Details

Hue is allocated recursively from a 0–360° budget at the root. At each internal node, the parent's budget is partitioned across its descendant edges in proportion to the number of leaves descended from each child; the colour reported for an edge or node is the midpoint of its assigned range. Saturation s = (nTip - nDesc) / (nTip - 1), where nDesc is the number of leaves descended from the node (including itself for tips), so the root is achromatic (s = 0) and every leaf is fully saturated (s = 1).

See also

CladeSizes(), DescendantEdges()

Other tree navigation: AncestorEdge(), CladeSizes(), DescendantEdges(), EdgeAncestry(), EdgeDistances(), ListAncestors(), MRCA(), MatchEdges(), NDescendants(), NodeDepth(), NodeNumbers(), NodeOrder(), RootNode()

Author

Martin R. Smith (martin.smith@durham.ac.uk)

Examples

tree <- BalancedTree(1:8) + PectinateTree(9:14)
tree <- ape::bind.tree(BalancedTree(1:8), PectinateTree(9:12), 8, 4)
paint <- PaintTree(tree)
plot(tree,
     edge.color = paint$edgeCol,
     tip.color = paint$tipCol,
     edge.width = 3)


# Colour-blind-safe variants
paintP <- PaintTree(tree, "protanopia")
plot(tree,
     edge.color = paintP$edgeCol,
     tip.color = paintP$tipCol,
     edge.width = 3)


paintT <- PaintTree(tree, "tritanopia")
plot(tree,
     edge.color = paintT$edgeCol,
     tip.color = paintT$tipCol,
     edge.width = 3)


# User-supplied palette function (greyscale)
grey_pal <- function(h, s) grey(1 - s * 0.8)
paintG <- PaintTree(tree, grey_pal)
plot(tree, edge.color = paintG$edgeCol, edge.width = 3)