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Plot posterior probabilities of states/ranges on phylogeny from densityMaps

Source: R/plot_densityMaps_overlay.R
plot_densityMaps_overlay.Rd

Plot on a time-calibrated phylogeny the evolution of a categorical trait/biogeographic ranges summarized from densityMaps typically generated with prepare_trait_data(). Each branch is colored according to the posterior probability of being in a given state/range. Color for each state/range are overlaid using transparency to produce a single plot for all states/ranges.

Usage

plot_densityMaps_overlay(
  densityMaps,
  colors_per_levels = NULL,
  add_ACE_pies = TRUE,
  cex_pies = 0.5,
  ace = NULL,
  ...,
  display_plot = TRUE,
  PDF_file_path = NULL
)

Arguments

densityMaps

List of objects of class "densityMap", typically generated with prepare_trait_data(), that contains a phylogenetic tree and associated posterior probability of being in a given state/range along branches. Each object (i.e., densityMap) corresponds to a state/range. If no color is provided for multi-area ranges, they will be interpolated.

colors_per_levels

Named character string. To set the colors to use to map each state/range posterior probabilities. Names = states/ranges; values = colors. If NULL (default), the color scale provided densityMaps will be used.

add_ACE_pies

Logical. Whether to add pies of posterior probabilities of states/ranges at internal nodes on the mapped phylogeny. Default = TRUE.

cex_pies

Numerical. To adjust the size of the ACE pies. Default = 0.5.

ace

Numerical matrix. To provide the posterior probabilities of ancestral states/ranges (characters) estimates (ACE) at internal nodes used to plot the ACE pies. Rows are internal nodes. Columns are states/ranges. Values are posterior probabilities of each state per node. Typically generated with prepare_trait_data() in the $ace slot. If NULL (default), the ACE are extracted from the densityMaps with a possible slight discrepancy with the actual tip states and estimated posterior probabilities of ancestral states.

...

Additional arguments to pass down to phytools::plotSimmap() to control plotting.

display_plot

Logical. Whether to display the plot generated in the R console. Default is TRUE.

PDF_file_path

Character string. If provided, the plot will be saved in a PDF file following the path provided here. The path must end with ".pdf".

Value

If display_plot = TRUE, the function plots a time-calibrated phylogeny displaying the evolution of a categorical trait/biogeographic ranges. If PDF_file_path is provided, the function exports the plot into a PDF file.

See also

phytools::plot.densityMap() phytools::plotSimmap()

Author

Maël Doré

Original functions by Liam Revell in R package phytools. Contact: liam.revell@umb.edu

Examples