Implementation of the algorithm in O(n) proposed in van der Ploeg, 2014 (https://onlinelibrary.wiley.com/doi/10.1002/spe.2213), adapted for plotting phylogenetic trees.
tidytree.Rcontains functions implementing a standalone version of the algo, with basic functionality. The main function for plotting a tree in "tidy" mode is as follows.
Usage:
plot.tidy(x, show.tip.label=T, cex=1, x.lim = NULL, y.lim = NULL,
verbose=T, ...)
Arguments:
x: an object of class ‘"phylo"’.
show.tip.label: a logical indicating whether to show the tip labels on
the phylogeny (defaults to ‘TRUE’, i.e. the labels are
shown).
cex: a numeric value giving the factor scaling of the tip and node
labels (Character EXpansion). The default is to take the
current value from the graphical parameters.
x.lim: a numeric vector of length one or two giving the limit(s) of
the x-axis. If ‘NULL’, this is computed with respect to
various parameters such as the string lengths of the labels
and the branch lengths. If a single value is given, this is
taken as the upper limit.
y.lim: same than above for the y-axis.
verbose: a logical value specifying whether the degree of compression
achieved (in %) should be reported. plot.phylo.Ris a fork of the same script in the ape package, but including a new "type" of phylogeny: "tidy". Refer to the help page of plot.phylo() in ape for details. Using this function with the tidy option is as simple as:
plot(tr, type="tidy", ...)All options available in plot.phylo can also be used here. Only the option for aligning tips (align.tip.label) will give ugly results because the new layout breaks the uniform distribution of the tips along the y-axis.
If you are curious about this new layout, here is how it looks like: On the left, the tree before compression (type="phylogram"). On the right the same tree after compression (type="tidy").
For questions/remarks/bug reports, please contact Damien de Vienne : damien.de-vienne@univ-lyon1.fr