nichevol_legend {nichevol}

Legends for niche evolution labels in phylogenetic trees

Description

Legends for niche evolution labels in phylogenetic trees

Usage

nichevol_legend(position, ancestor_line = FALSE,
  ancestor_legend = c("Uncertain", "Present"),
  evol_legend = c("No change", "Retraction", "Expansion"),
  ancestor_col = c("#d9d9d9", "#252525"),
  evol_col = c("#b2df8a", "#984ea3", "#4daf4a"),
  pch = 22, pt.cex = 2.2, lty = 1, lwd = 1, cex = 1, 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)).

ancestor_line

whether or not ancestor line was plotted. Default = FALSE.

ancestor_legend

(character) vector of length = two indicating the text to identify environments with uncertain presence and true presence of the species. Default = c("Uncertain", "Present").

evol_legend

(character) vector of length = three indicating the text to identify environments where niches have not changed, have retracted or expanded. Default = c("No change", "Retraction", "Expansion").

ancestor_col

vector of two colors to represent what is indicated in ancestor_legend. Default = c("#d9d9d9", "#252525").

evol_col

vector of three colors to represent what is indicated in evol_legend. Default = c("#b2df8a", "#984ea3", "#4daf4a").

pch

point type as in points. Default = 22.

pt.cex

size of symbol (points). Default = 2.2.

lty

line type see par. Default = 1.

lwd

line width see par. Default = 1.

cex

size of all elements in legend see par. Default = 1.

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)
nichevol_labels(tree5, rec_tab, height = 0.6)
nichevol_legend(position = "bottomleft", cex = 0.7)