append2tips: Append Symbols or Text to Tip Labels

In fmichonneau/phyloch: Tools for phylogenetics and taxonomy

Description

This function allows to add text or symbols to the tip labels of a phylogenetic tree

Usage

append2tips(phy, tips, offset, align = FALSE,
	grid = FALSE, col = "red", text = NULL, pch = NULL, cex, ...)

Arguments

phy	an object of class phylo.
tips	a vector of mode "numeric", giving the tip numbers to which append text or symbols. If missing, all tips are used.
offset	a real, used to control the horizontal offset of text or symbols from the tip labels of the phylogenetic tree.
align	logical, if TRUE text or symbols are horizontal aligned.
grid	logial, if TRUE dotted lines are plotted as a horizontal grid to aid visual orientation.
col	a character string, setting the color for text of symbols
text	a character string, giving the text to be appended to the tip labels
pch	an integer, specifying the symbol used (see par).
cex	a real number, giving the character expension (see par). If missing, cex is taking from the previous call of plot.phylo.
...	further graphical parameters (from par), such as srt, family and xpd.

Details

Currently, append2tips is will work only for plot.phylo using types "phylogram" or "cladogram" and directions "rightwards" or "leftwards".

Value

None.

Author(s)

Christoph Heibl

See Also

plot.phylo, tiplabels, taxo.fonts

Examples

# phylogeny of true vipers
# ------------------------
data(viperidae)
plot.phylo(viperidae, cex = 0.8, label.offset = 0.02, x.lim = 1.5)
NTips <- length(viperidae$tip.label)
append2tips(viperidae, text = 
	paste("A", 1:NTips, sep = "-"), col = "orange")
append2tips(viperidae, tips <- c(5, 7:9, 14), 
	text = rep("xxx", 5), col = "slateblue")
append2tips(viperidae, pch = 23, col = rainbow(NTips))
append2tips(viperidae, pch = 21, col = "grey50", 	
    align = TRUE, grid = TRUE)

fmichonneau/phyloch documentation built on May 16, 2019, 1:45 p.m.