taxo.fonts: Font Types for Tip Labels

In fmichonneau/phyloch: Tools for phylogenetics and taxonomy

Description

This function can be used to render scientific names taxonomically correctly when plotting phylogenies.

Usage

taxo.fonts(phy, cex, offset, col, align = FALSE, auto.correction = 
    TRUE, s = c("spec.", "subspec.", "var.", "cf.", "agg.",
    "syn."), lty = 3, lcol = "grey25")

Arguments

phy	An object of class phylo.
cex	A real number, giving the character expension (see par).
offset	A real number giving the horizontal offset between tips and tip labels.
col	A character string, giving the color(s) to be used for the tip labels).
align	Logical, if TRUE, the tip labels will be left-justified according to the largest root-tip distance + offset.
auto.correction	Logical; if TRUE, tip labels will be corrected for non-official abbreviations.
s	A vector of mode character containing the strings that will be printed in plain font type.
lty	A numeric, giving the line type if align = TRUE. The plotting of the lines can be suppressed with lty = 0. See par for more options.
lcol	A character string, giving the line color if align = TRUE.

Details

Use plot.phylo with the tip.color argument set to 0 to suppress plotting of the tip labels. This gets you the correct extension of the plotting region, which would not be the case with show.tip.label = FALSE.

Value

None.

Author(s)

Christoph Heibl

See Also

plot.phylo

Examples

# molecular phylogeny of Eurasian vipers:
# ---------------------------------------
data(viperidae)

# plot phylogeny: strings contained in 's' will be 
# in plain font type and the corresponding tips labels 
# colored brown; note the use of 'tip.color = 0' in 
# 'plot.phylo'
# ----------------------------------------------------
s  <-  c("ssp.", "var.", "spec.", "cf.", "agg.", "syn.")
tcol <- tip.color(viperidae, s, col = "brown") 
plot.phylo(viperidae, tip.color = 0)
taxo.fonts(viperidae, col = tcol)

# align tip labels:
# here we need to set the x.lim argument in plot.phylo
# ----------------------------------------------------
plot.phylo(viperidae, tip.color = 0, x.lim = c(0, 1.3)) 
taxo.fonts(viperidae, align = TRUE, offset = 0.1)

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