plot_phylo_comb: Plot shifts of diversifcation on a phylogeny

In hmorlon/PANDA: Phylogenetic ANalyses of DiversificAtion

Plot shifts of diversifcation on a phylogeny

Description

Plots the phylogeny with colored branches according to shifts of diversification.

Usage

plot_phylo_comb(phylo, data, sampling.fractions, shift.res = NULL,
                combi, backbone.option = "crown.shift",
                main = NULL, col.sub = NULL, col.bck = "black",
                lty.bck = 1, tested_nodes = F, lad = T,
                leg = T, text.cex = 1, pch.cex = 1, ...)

Arguments

phylo	an object of type 'phylo' (see ape documentation)
data	a data.frame containing a database of monophyletic groups for which potential shifts can be tested. This database should be based on taxonomy, ecology or traits and must contain a column named "Species" with species names as in phylo.
sampling.fractions	the output resulting from get.sampling.fractions.
shift.res	the output resulting from shift.estimates or NULL (default). This latter case allows to represent combinations only from the output of get.comb.shift by specifying the combination (see argument combi).
combi	character or numeric. If shift.res is provided, this argument is a numeric and corresponds to the rank of the combination in the global comparison (shift.res$total). If shift.res is NULL, this argument should be a character giving a combination of node IDs as in get.comb.shift output. This latter manner to specify combination allows to visualize a combination of shifts before having results.
backbone.option	type of the backbone analysis (see backbone.option in shift.estimates for more details): "stem.shift": the stems of subclades are included in subclade analyses; "crown.shift": the stems of subclades are included in the backbone analysis (Default).
main	Character. The name of the plot. Default is NULL and the combination rank with AICc will be printed if shift.res is not NULL.
col.sub	character. A vector to specify colors of subclade(s). Can be let NULL (see details).
col.bck	character. A vector to specify colors of backbone(s). Default is "black" for simple backbone (see details).
lad	bolean. Allows to ladderize the tree.
leg	bolean. If TRUE, legend of the selected combination is added to the plot with names from data and best model names. Default is TRUE. The position is automatically adjusted in function of lad argument.
lty.bck	numeric. Define lty for the backbone.
tested_nodes	bolean. If TRUE, all the tested nodes are highlighted by a red point.
text.cex	numeric. Define the size of legend text.
pch.cex	numeric. Define the size of points if tested_nodes = TRUE
...	further arguments to be passed to plot or to plot.phylo.

Details

If col.sub is not specified, color vector for subclades is c(c(brewer.pal(8, "Dark2"),brewer.pal(8, "Set1"),"darkmagenta","dodgerblue2", "orange", "forestgreen")). For multiple backbone, default vector is c("blue4", "orange4", "red4", "grey40", "coral4", "deeppink4", "khaki4", "darkolivegreen", "darkslategray",”black”). ... allows to set different graphical parameters from plot.phylo such as cex for size of tip labels or edge.width for the thickness of the phylogeny edges.

Value

plot the phylogeny and returns the same invisible object as plot.phylo.

Author(s)

Nathan Mazet

References

Mazet, N., Morlon, H., Fabre, P., Condamine, F.L., (2023). Estimating clade‐specific diversification rates and palaeodiversity dynamics from reconstructed phylogenies. Methods in Ecology and in Evolution 14, 2575–2591. https://doi.org/10.1111/2041-210X.14195

See Also

shift.estimates

Examples

# loading data
data("Cetacea")
data("taxo_cetacea")

taxo_cetacea_no_genus <- taxo_cetacea[names(taxo_cetacea) != "Genus"]

# main procedure
f_cetacea <- get.sampling.fractions(phylo = Cetacea, lad = FALSE,
                                    data = taxo_cetacea_no_genus,
                                    plot = TRUE, cex = 0.3)

comb.shift_cetacea <- get.comb.shift(phylo = Cetacea,
                                     data = taxo_cetacea_no_genus,
                                     sampling.fractions = f_cetacea,
                                     Ncores = 4)

# use of plot_phylo_comb
# without shift.estimates results but with comb.shift_cetacea

plot_phylo_comb(phylo = Cetacea,
                data = taxo_cetacea,
                sampling.fractions = f_cetacea,
                combi = comb.shift_cetacea[15],
                label.offset = 0.3,
                main = "", lad = FALSE ,cex = 0.4)

hmorlon/PANDA documentation built on April 24, 2024, 3:27 a.m.