delim_autoplot2: Plot Phylogenetic Trees With Species Delimitation Partitions

In delimtools: Helper Functions for Species Delimitation Analysis

Plot Phylogenetic Trees With Species Delimitation Partitions

Description

delim_autoplot2() returns a phylogenetic tree plotted using ggtree alongside with a customized tile plot using geom_tile combined by wrap_plots.

Usage

delim_autoplot2(
  delim,
  tr,
  consensus = TRUE,
  n_match = NULL,
  delim_order = NULL,
  tbl_labs,
  species,
  hexpand = 0.1,
  widths = c(0.5, 0.2)
)

Arguments

delim	Output from delim_join.
tr	A treedata object. Both phylogram and ultrametric trees are supported.
consensus	Logical. Should the majority-vote consensus to be estimated?
n_match	An Integer. If consensus = TRUE, threshold for majority-vote calculations. See delim_consensus for details.
delim_order	A character vector of species delimitation names ordered by user. Default to NULL.
tbl_labs	A tbl_df of customized labels for tree plotting. The first column must match tip labels of the tr object, while the second column should have customized labels.
species	column name in tbl_labs which contains species names for each tip of the tree.
hexpand	Numeric. Expand xlim of tree by a ratio of x axis range. Useful if tiplabels become truncated when plotting. Default to 0.1.
widths	A numeric vector containing the relative widths of the tree and species delimitation bars. See wrap_plots for details. Defaults to c(0.5, 0.2).

Details

delim_autoplot2() is a wrapper for tree plotting with associated data implemented using ggtree, ggplot2, and patchwork. If consensus = TRUE, a consensus bar will be plotted next to the species delimitation plot, summarizing partitions across samples. If no consensus is reached, an "X" will be plotted instead. This function is a modified version of delim_autoplot which plots species partitions using a black and grey color scheme.

Value

A patchwork object.

Author(s)

Pedro S. Bittencourt, Rupert A. Collins.

Examples

# create labels
labs <- geophagus_info |> dplyr::select(gbAccession, scientificName)

# view partitions using an ultrametric tree
p <- delim_autoplot2(geophagus_delims,
  geophagus_beast,
  tbl_labs = labs,
  species = "scientificName"
)
p

# view partitions using a phylogram
p1 <- delim_autoplot2(geophagus_delims,
  geophagus_raxml,
  tbl_labs = labs,
  species = "scientificName"
)

delimtools documentation built on April 3, 2025, 9:28 p.m.