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Plot trait/range evolution vs. diversification rates and regime shifts on phylogeny

Source: R/plot_traits_vs_rates_on_phylogeny_for_focal_time.R
plot_traits_vs_rates_on_phylogeny_for_focal_time.Rd

Plot two mapped phylogenies with evolutionary data with branches cut off at focal_time.

  • Left facet: plot the evolution of trait data/geographic ranges on the left time-calibrated phylogeny.

    • For continuous data: Each branch is colored according to the estimates value of the traits.

    • For categorical and biogeographic 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.

  • Right facet: plot the evolution of diversification rates and location of regime shits estimated from a BAMM (Bayesian Analysis of Macroevolutionary Mixtures). Each branch is colored according to the estimated rates of speciation, extinction, or net diversification stored in an object of class bammdata. Rates can vary along time, thus colors evolved along individual branches.

This function is a wrapper multiple plotting functions:

Usage

plot_traits_vs_rates_on_phylogeny_for_focal_time(
  deepSTRAPP_outputs,
  focal_time = NULL,
  color_scale = NULL,
  colors_per_levels = NULL,
  add_ACE_pies = TRUE,
  cex_pies = 0.5,
  rate_type = "net_diversification",
  keep_initial_colorbreaks = FALSE,
  add_regime_shifts = TRUE,
  configuration_type = "MAP",
  sample_index = 1,
  adjust_size_to_prob = TRUE,
  regimes_fill = "grey",
  regimes_size = 1,
  regimes_pch = 21,
  regimes_border_col = "black",
  regimes_border_width = 1,
  ...,
  display_plot = TRUE,
  PDF_file_path = NULL
)

Arguments

deepSTRAPP_outputs

List of elements generated with run_deepSTRAPP_for_focal_time(), that summarize the results of a STRAPP test for a specific time in the past (i.e. the focal_time). deepSTRAPP_outputs can also be extracted from the output of run_deepSTRAPP_over_time() that run the whole deepSTRAPP workflow over multiple time-steps.

focal_time

Numerical. (Optional) If deepSTRAPP_outputs comprises results over multiple time-steps (i.e., output of run_deepSTRAPP_over_time(), this is the time of the STRAPP test targeted for plotting.

color_scale

Vector of character string. List of colors to use to build the color scale with grDevices::colorRampPalette() showing the evolution of a continuous trait. From lowest values to highest values. (For continuous trait data only)

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. (For categorical and biogeographic data only)

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.

rate_type

A character string specifying the type of diversification rates to plot. Must be one of 'speciation', 'extinction' or 'net_diversification' (default).

keep_initial_colorbreaks

Logical. Whether to keep the same color breaks as used for the most recent focal time. Typically, the current time (t = 0). This will only works if you provide the output of run_deepSTRAPP_over_time() as deepSTRAPP_outputs. Default = FALSE.

add_regime_shifts

Logical. Whether to add the location of regime shifts on the phylogeny (Step 2). Default is TRUE.

configuration_type

A character string specifying how to select the location of regime shifts across posterior samples.

  • configuration_type = "MAP": Use the average locations recorded in posterior samples with the Maximum A Posteriori probability (MAP) configuration. This regime shift configuration is the most frequent configuration among the posterior samples (See BAMMtools::getBestShiftConfiguration()). This is the default option.

  • configuration_type = "MSC": Use the average locations recorded in posterior samples with the Maximum Shift Credibility (MSC) configuration. This regime shift configuration has the highest product of marginal probabilities across branches (See BAMMtools::maximumShiftCredibility()).

  • configuration_type = "index": Use the configuration of a unique posterior sample those index is provided in sample_index.

sample_index

Integer. Index of the posterior samples to use to plot the location of regime shifts. Used only if configuration_type = index. Default = 1.

adjust_size_to_prob

Logical. Whether to scale the size of the symbols showing the location of regime shifts according to the marginal shift probability of the shift happening on each location/branch. This will only works if there is an $MSP_tree element summarizing the marginal shift probabilities across branches in the BAMM_object. Default is TRUE.

regimes_fill

Character string. Set the color of the background of the symbols showing the location of regime shifts. Equivalent to the bg argument in BAMMtools::addBAMMshifts(). Default is "grey".

regimes_size

Numerical. Set the size of the symbols showing the location of regime shifts. Equivalent to the cex argument in BAMMtools::addBAMMshifts(). Default is 1.

regimes_pch

Integer. Set the shape of the symbols showing the location of regime shifts. Equivalent to the pch argument in BAMMtools::addBAMMshifts(). Default is 21.

regimes_border_col

Character string. Set the color of the border of the symbols showing the location of regime shifts. Equivalent to the col argument in BAMMtools::addBAMMshifts(). Default is "black".

regimes_border_width

Numerical. Set the width of the border of the symbols showing the location of regime shifts. Equivalent to the lwd argument in BAMMtools::addBAMMshifts(). Default is 1.

...

Additional graphical arguments to pass down to phytools::plot.contMap(), phytools::plotSimmap(), plot_densityMaps_overlay(), BAMMtools::plot.bammdata(), BAMMtools::addBAMMshifts(), and par().

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 displays a plot with two facets in the R console:

  • (Left) A time-calibrated phylogeny displaying the evolution of trait/biogeographic data.

  • (Right) A time-calibrated phylogeny displaying diversification rates and regime shifts.

If PDF_file_path is provided, the plot will be exported in a PDF file.

Details

The main input deepSTRAPP_outputs is the typical output of run_deepSTRAPP_for_focal_time(). It provides information on results of a STRAPP test performed at a given focal_time, and can also encompass updated phylogenies with mapped trait evolution and diversification rates and regimes shifts if appropriate arguments are set.

  • return_updated_trait_data_with_Map must be set to TRUE so that the trait data extracted for the given focal_time and the updated version of mapped phylogeny (contMap/densityMaps) are returned among the outputs under $updated_trait_data_with_Map. The updated contMap/densityMaps consists in cutting off branches and mappings that are younger than the focal_time.

  • return_updated_BAMM_object must be set to TRUE so that the updated_BAMM_object with phylogeny and mapped diversification rates cut-off at the focal_time are returned among the outputs under $updated_BAMM_object.

$MAP_BAMM_object and $MSC_BAMM_object elements are required in $updated_BAMM_object to plot regime shift locations following the "MAP" or "MSC" configuration_type respectively. A $MSP_tree element is required to scale the size of the symbols showing the location of regime shifts according marginal shift probabilities. (If adjust_size_to_prob = TRUE).

Alternatively, the main input deepSTRAPP_outputs can be the output of run_deepSTRAPP_over_time(), providing results of STRAPP tests over multiple time-steps. In this case, you must provide a focal_time to select the unique time-step used for plotting.

  • return_updated_trait_data_with_Map must be set to TRUE so that the trait data extracted and the updated version of mapped phylogenies (contMap/densityMaps) are returned among the outputs under $updated_trait_data_with_Map_over_time.

  • return_updated_BAMM_object must be set to TRUE so that the BAMM_objects with phylogeny and mapped diversification rates cut-off at the specified time-steps are returned among the outputs under $updated_BAMM_objects_over_time.

For plotting all time-steps at once, see plot_traits_vs_rates_on_phylogeny_over_time().

See also

phytools::plot.densityMap() plot_densityMaps_overlay() plot_BAMM_rates()

Functions in deepSTRAPP needed to produce the deepSTRAPP_outputs as input: run_deepSTRAPP_for_focal_time() run_deepSTRAPP_over_time() Function in deepSTRAPP to plot all time-steps at once: plot_traits_vs_rates_on_phylogeny_over_time()

Author

Maël Doré

Examples