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Plot a phylogeny with species abundances and phylogenetic diversity

Source: R/plot-extra.R
plot_phylo.Rd

Draws a rectangular phylogram of a phylo tree with ggplot2. With data, a column of dots per site beside the tips shows each species' relative abundance at that site. With highlight, the branches leading to the species found at one site are coloured: their summed length is that site's Faith's phylogenetic diversity (PD; Faith 1992), the quantity behind q = 0 phylogenetic Hill numbers (Chao et al. 2010).

Usage

plot_phylo(
  tree,
  data = NULL,
  site = site,
  species = species,
  abundance = NULL,
  highlight = NULL,
  tip_labels = TRUE,
  theme = theme_tidydiversity(grid = "none")
)

Arguments

tree

A rooted tree of class phylo, for example from ape::read.tree(). Without branch lengths every branch has length 1.

data

Optional data frame of species records by site.

site, species, abundance

Columns of data. Without abundance, each row counts as one record.

highlight

Optional site whose branches to colour.

tip_labels

Draw the tip labels (underscores become spaces).

theme

A ggplot2 theme, by default theme_tidydiversity().

Value

A ggplot object.

References

Faith, D. P. (1992). Conservation evaluation and phylogenetic diversity. Biological Conservation, 61, 1-10. doi:10.1016/0006-3207(92)91201-3

Chao, A., Chiu, C.-H. and Jost, L. (2010). Phylogenetic diversity measures based on Hill numbers. Philosophical Transactions of the Royal Society B, 365, 3599-3609. doi:10.1098/rstb.2010.0272

Examples

# A taxonomic tree (family / genus / species) for the Mt Wilhelm frogs
frogs <- png_frogs
frogs$genus <- sub(" .*", "", frogs$scientific_name)
frogs$tip <- gsub(" ", "_", frogs$scientific_name)
tax <- unique(as.data.frame(frogs[c("family", "genus", "tip")]))
tax[] <- lapply(tax, factor)
tree <- ape::compute.brlen(ape::as.phylo(~ family / genus / tip, data = tax))
plot_phylo(tree, frogs, species = tip, highlight = "MW0200")