niche_legend: Legends for niche labels in phylogenetic trees

In nichevol: Tools for Ecological Niche Evolution Assessment Considering Uncertainty

Legends for niche labels in phylogenetic trees

Description

Legends for niche labels in phylogenetic trees

Usage

niche_legend(position, legend = c("Uncertain", "Present", "Not present"),
  pch = 22, pt.bg = c("#969696", "#e41a1c", "#377eb8"),
  col = "transparent", pt.cex = 2.2, bty = "n", ...)

Arguments

position	(character or numeric) position of legend. If character, part of the plot (e.g., "topleft"), see legend. If numeric, vector of two values indicating x and y position (e.g., c(0.1, 6)).
legend	(character) vector of length = three indicating the text to identify environments with uncertain presence, presence, and absence of the species. Default = c("Uncertain", "Present", "Not present").
pch	point type as in points. Default = 22.
pt.bg	colors to represent what is in legend. Default = c("#969696", "#e41a1c", "#377eb8").
col	border of symbol (points). Default = "transparent".
pt.cex	size of symbol (points). Default = 2.2.
bty	legend border type. Default = "n".
...	Other arguments from function legend other than the ones described above.

Examples

# a simple tree
data("tree5", package = "nichevol")

# a matrix of niche charactes (1 = present, 0 = absent, ? = unknown)
dataTable <- cbind("241" = rep("1", length(tree5$tip.label)),
                   "242" = rep("1", length(tree5$tip.label)),
                   "243" = c("1", "1", "0", "0", "0"),
                   "244" = c("1", "1", "0", "0", "0"),
                   "245" = c("1", "?", "0", "0", "0"))
rownames(dataTable) <- tree5$tip.label

# list with two objects (tree and character table)
treeWdata <- geiger::treedata(tree5, dataTable)

# Maximum parsimony reconstruction
rec_tab <- smooth_rec(bin_par_rec(treeWdata))

# plotting and adding labels and legend
ape::plot.phylo(tree5, label.offset = 0.04)
niche_labels(tree5, rec_tab, height = 0.6)
niche_legend(position = "topleft", cex = 0.7)

nichevol documentation built on March 31, 2023, 5:38 p.m.