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Plot Phylogenetic Trees With Species Delimitation Partitions

Source: R/delim_autoplot2.R
delim_autoplot2.Rd

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).

Value

A patchwork object.

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.

Author

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"
)
#> Warning: Argument `delim_order` not provided. Using default order from `delim`.
#> Warning: ⚠ `n_match` was not found. Using `n_match= 5` instead.
p


# view partitions using a phylogram
p1 <- delim_autoplot2(geophagus_delims,
  geophagus_raxml,
  tbl_labs = labs,
  species = "scientificName"
)
#> Warning: Argument `delim_order` not provided. Using default order from `delim`.
#> Warning: ⚠ `n_match` was not found. Using `n_match= 5` instead.