phenogram {phytools}

Plot traitgram (phenogram)

Description

Plots a phylogenetic traitgram (Evans et al., 2009).

Usage

phenogram(tree, x, fsize=1.0, ftype="reg", colors=NULL, axes=list(),
   add=FALSE, ...)

Arguments

tree

an object of class "phylo", with or without a mapped discrete character.

x

a vector containing the states at the tips or the states at all the tips and the internal nodes of the tree.

fsize

relative font size for tip labels.

ftype

font type - options are "reg", "i" (italics), "b" (bold), or "bi" (bold-italics).

colors

colors for plotting the mapped character (if available) in tree. If no character is mapped on the tree, then a single color for all the branches of the tree can be provided.

axes

list of axis dimensions. Items are time and trait.

add

optional logical value indicating whether to add to an open plot. If TRUE, then new axes will not be plotted.

...

optional arguments including xlim, ylim, log, main, sub, xlab, ylab, asp, type, lty, lwd, offset, and digits are as in plot.default or par. Note that axes overrides xlim and ylim. spread.labels is a logical value indicating whether or not to minimize tip label overlap (default is TRUE); spread.cost is a numeric vector indicating the relative penalty to be used for label overlap and deviance, respectively (if spread.labels=TRUE); spread.range is the range over which to (potentially) spread the labels - note that if labels do not overlap, not all of that range will be used; finally, link is a numeric value by which to offset the tip labels, linking them to the tips with a dashed line (default is 0, if spread.labels=FALSE, or 10% of the total tree length otherwise). The optional argument offsetFudge "fudges" the computation of label offset in scaling xlim. It is 1.37, which is the correct fudge in the Windows R GUI, but this may need to be changed in other systems. hold indicates whether (or not) the output to the graphical device should be held using dev.hold before plotting (defaults to hold=TRUE). quiet suppresses some system messages if set to quiet=TRUE.

Details

Function plots a traitgram (Evans et al. 2009), that is, a projection of the phylogenetic tree in a space defined by phenotype (on the y axis) and time (on the x). If a discrete character is mapped on the tree this will also be plotted.

For spread.labels=TRUE numerical optimization is performed to optimize the distribution of the labels vertically, where the solution depends on the vector spread.cost containing the cost of overlap (first) and the cost of deviation from the vertical position of the tip. Note that because this is done via numerical optimization, plotting may hang briefly while the best solution is found (especially for large trees).

Value

Plots a traitgram, optionally with a mapped discrete character, and (invisibly) returns a matrix containing the coordinates of the plotted tip labels.

Author(s)

Liam Revell [e-mail]

References

Evans, M. E. K., Smith, S. A., Flynn, R. S., Donoghue, M. J. (2009) Climate, niche evolution, and diversification of the "bird-cage" evening primroses (Oenothera, sections Anogra and Kleinia). American Naturalist, 173, 225-240.

Revell, L. J. (2013) Two new graphical methods for mapping trait evolution on phylogenies. Methods in Ecology and Evolution, 4, 754-759.

Revell, L. J. (2014) Graphical methods for visualizing comparative data on phylogenies. Chapter 4 in Modern phylogenetic comparative methods and their application in evolutionary biology: Concepts and practice (L. Z. Garamszegi ed.), pp. 77-103.

Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.

Revell, L. J., K. Schliep, E. Valderrama, and J. E. Richardson (2018) Graphs in phylogenetic comparative analysis: Anscombe's quartet revisited. Methods in Ecology and Evolution, 9, 2145-2154.

Examples

## load data from Garland et al. (1992)
data(mammal.tree)
data(mammal.data)
## extract character of interest
ln.bodyMass<-log(setNames(mammal.data$bodyMass,
  rownames(mammal.data)))
## plot traitgram
phenogram(mammal.tree,ln.bodyMass,ftype="i",
  spread.cost=c(1,0),fsize=0.7,color=palette()[4],
  xlab="time (ma)",ylab="log(body mass)",las=1)