TreeTools (version 2.4.1)

PaintTree: Colour a tree by topology

Description

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")

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.

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.

Author

Martin R. Smith ()

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()

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)