Plot Phylogenetic Trees With Species Delimitation Partitions

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

Usage

delim_autoplot(
  delim,
  tr,
  consensus = TRUE,
  n_match = NULL,
  delim_order = NULL,
  tbl_labs = NULL,
  col_vec = NULL,
  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.
col_vec: A color vector for species delimitation partitions. See delim_brewer for customized color palette options.
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_autoplot() 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.

Author

Pedro S. Bittencourt, Rupert A. Collins.

Examples

# view partitions using an ultrametric tree
p <- delim_autoplot(geophagus_delims, geophagus_beast)
#> Warning: ⚠ Argument `tbl_labs` not provided. Using tiplabels instead.
#> Warning: `aes_()` was deprecated in ggplot2 3.0.0.
#> ℹ Please use tidy evaluation idioms with `aes()`
#> ℹ The deprecated feature was likely used in the ggtree package.
#>   Please report the issue at <https://github.com/YuLab-SMU/ggtree/issues>.
#> Warning: Arguments in `...` must be used.
#> ✖ Problematic arguments:
#> • as.Date = as.Date
#> • yscale_mapping = yscale_mapping
#> • hang = hang
#> • color = "grey50"
#> • size = 1
#> ℹ Did you misspell an argument name?
#> Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
#> ℹ Please use `linewidth` instead.
#> ℹ The deprecated feature was likely used in the ggtree package.
#>   Please report the issue at <https://github.com/YuLab-SMU/ggtree/issues>.
#> Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
#> ℹ Please use tidy evaluation idioms with `aes()`.
#> ℹ See also `vignette("ggplot2-in-packages")` for more information.
#> ℹ The deprecated feature was likely used in the ggtree package.
#>   Please report the issue at <https://github.com/YuLab-SMU/ggtree/issues>.
#> Warning: ⚠ Argument `delim_order` not provided. Using default order from
#> `geophagus_delims`.
#> Warning: ⚠ Argument `col_vec` not provided. Customizing one using `delim_brewer()`.
#> ℹ Please use `delimtools::delim_brewer()` to create even better colour
#>   palettes!
#> Warning: ⚠ `n_match` was not found. Using `n_match= 4` instead.
p


# view partitions using a phylogram
p1 <- delim_autoplot(geophagus_delims, geophagus_raxml)
#> Warning: ⚠ Argument `tbl_labs` not provided. Using tiplabels instead.
#> Warning: Arguments in `...` must be used.
#> ✖ Problematic arguments:
#> • as.Date = as.Date
#> • yscale_mapping = yscale_mapping
#> • hang = hang
#> • color = "grey50"
#> • size = 1
#> ℹ Did you misspell an argument name?
#> Warning: ⚠ Argument `delim_order` not provided. Using default order from
#> `geophagus_delims`.
#> Warning: ⚠ Argument `col_vec` not provided. Customizing one using `delim_brewer()`.
#> ℹ Please use `delimtools::delim_brewer()` to create even better colour
#>   palettes!
#> Warning: ⚠ `n_match` was not found. Using `n_match= 4` instead.