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

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. Colors 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 shifts 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 evolve along individual branches.

This function is a wrapper of multiple plotting functions:

For continuous traits: plot_contMap()
For categorical and biogeographic data: plot_densityMaps_overlay()
For BAMM rates and regime shifts: plot_BAMM_rates()

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,
  rate_type = "net_diversification",
  keep_initial_colorbreaks = FALSE,
  add_regime_shifts = TRUE,
  configuration_type = "MAP",
  sample_index = 1,
  regimes_fill = "grey",
  regimes_size = 1,
  regimes_pch = 21,
  regimes_border_col = "black",
  regimes_border_width = 1,
  ...,
  cex_pies = 0.5,
  adjust_size_to_prob = TRUE,
  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. This must contain an updated contMap/densityMaps and updated BAMM_object (see Details section below).

focal_time

Numeric. (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

Character vector. 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 in 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.

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 work 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 whose 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.

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

Numeric. 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

Numeric. 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(). If provided, par.reset is ignored with a message. See plot_BAMM_rates() for details.

cex_pies

Numeric. To adjust the size of the ACE pies. Default = 0.5. Provide the full argument name to avoid ambiguity with the cex graphical argument.

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 work if there is an $MSP_tree element summarizing the marginal shift probabilities across branches in the BAMM_object. Default is TRUE. Provide the full argument name to avoid ambiguity with the adj graphical argument.

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 regime shifts if appropriate arguments are set.

return_updated_Maps must be set to TRUE so that the updated version of mapped phylogeny (contMap/densityMaps) for the given focal_time is returned among the outputs under $updated_Maps. The update of the contMap/densityMaps consists of cutting off branches and mappings that are younger than the focal_time. contMap/densityMaps must have been provided among the inputs to run_deepSTRAPP_for_focal_time() in the first place.
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 to 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_Maps must be set to TRUE so that the updated version of mapped phylogenies (contMap/densityMaps) are returned among the outputs under $updated_Maps_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().

Author

Maël Doré

Examples

if (deepSTRAPP::is_dev_version())
{
 # ----- Example 1: Continuous trait ----- #
 ## Load data

 # Load trait df
 data(Ponerinae_trait_tip_data, package = "deepSTRAPP")
 # Load phylogeny with old calibration
 data(Ponerinae_tree_old_calib, package = "deepSTRAPP")

 # Load the BAMM_object summarizing 1000 posterior samples of BAMM
 data(Ponerinae_BAMM_object_old_calib, package = "deepSTRAPP")
 ## This dataset is only available in development versions installed from GitHub.
 # It is not available in CRAN versions.
 # Use remotes::install_github(repo = "MaelDore/deepSTRAPP") to get the latest development version.

 ## Prepare trait data

 # Extract continuous trait data as a named vector
 Ponerinae_cont_tip_data <- setNames(object = Ponerinae_trait_tip_data$fake_cont_tip_data,
                                     nm = Ponerinae_trait_tip_data$Taxa)

 # Select a color scheme from lowest to highest values
 color_scale = c("darkgreen", "limegreen", "orange", "red")

 # Get Ancestral Character Estimates based on a Brownian Motion model
 # To obtain values at internal nodes
 Ponerinae_ACE <- phytools::fastAnc(tree = Ponerinae_tree_old_calib, x = Ponerinae_cont_tip_data)

  # (May take several minutes to run)
 # Run a Stochastic Mapping based on a Brownian Motion model
 # to interpolate values along branches and obtain a "contMap" object
 Ponerinae_contMap <- phytools::contMap(Ponerinae_tree_old_calib, x = Ponerinae_cont_tip_data,
                                        res = 100, # Number of time steps
                                        plot = FALSE)
 # Plot contMap = stochastic mapping of continuous trait
 plot_contMap(contMap = Ponerinae_contMap,
              color_scale = color_scale)

 ## Set focal time to 10 Mya
 focal_time <- 10

 ## Run deepSTRAPP on net diversification rates for focal time = 10 Mya.

 Ponerinae_deepSTRAPP_cont_old_calib_10My <- run_deepSTRAPP_for_focal_time(
   contMap = Ponerinae_contMap,
   ace = Ponerinae_ACE,
   tip_data = Ponerinae_cont_tip_data,
   trait_data_type = "continuous",
   BAMM_object = Ponerinae_BAMM_object_old_calib,
   focal_time = focal_time,
   uncertainty_strategy = "rates_only",
   return_updated_Maps = TRUE,
   return_updated_BAMM_object = TRUE)

 ## Explore output
 str(Ponerinae_deepSTRAPP_cont_old_calib_10My, max.level = 1)

 ## Plot updated contMap vs. updated diversification rates
 plot_traits_vs_rates_on_phylogeny_for_focal_time(
    deepSTRAPP_outputs = Ponerinae_deepSTRAPP_cont_old_calib_10My,
    keep_initial_colorbreaks = TRUE, # To use the same color breaks as for t = 0 My
    color_scale = c("limegreen", "orange", "red"), # Adjust color scale on contMap
    legend = TRUE, labels = TRUE, # Show legend and label on BAMM plot
    cex = 0.7) # Adjust label size on contMap
    # PDF_file_path = "Updated_maps_cont_10My.pdf") 

 # ----- Example 2: Biogeographic data ----- #

 ## Load data

 # Load phylogeny
 data(Ponerinae_tree_old_calib, package = "deepSTRAPP")
 # Load trait df
 data(Ponerinae_binary_range_table, package = "deepSTRAPP")

 # Load the BAMM_object summarizing 1000 posterior samples of BAMM
 data(Ponerinae_BAMM_object_old_calib, package = "deepSTRAPP")
 ## This dataset is only available in development versions installed from GitHub.
 # It is not available in CRAN versions.
 # Use remotes::install_github(repo = "MaelDore/deepSTRAPP") to get the latest development version.

 ## Prepare range data for Old World vs. New World

 # No overlap in ranges
 table(Ponerinae_binary_range_table$Old_World, Ponerinae_binary_range_table$New_World)

 Ponerinae_NO_tip_data <- stats::setNames(object = Ponerinae_binary_range_table$Old_World,
                                      nm = Ponerinae_binary_range_table$Taxa)
 Ponerinae_NO_tip_data <- as.character(Ponerinae_NO_tip_data)
 Ponerinae_NO_tip_data[Ponerinae_NO_tip_data == "TRUE"] <- "O" # O = Old World
 Ponerinae_NO_tip_data[Ponerinae_NO_tip_data == "FALSE"] <- "N" # N = New World
 names(Ponerinae_NO_tip_data) <- Ponerinae_binary_range_table$Taxa
 table(Ponerinae_NO_tip_data)

 colors_per_levels <- c("mediumpurple2", "peachpuff2")
 names(colors_per_levels) <- c("N", "O")

  # (May take several minutes to run)

 # Load ape and BioGeoBEARS to use models internally
 library(ape)
 library(BioGeoBEARS)

 ## Run evolutionary models
 Ponerinae_biogeo_data <- prepare_trait_data(
     tip_data = Ponerinae_NO_tip_data,
     trait_data_type = "biogeographic",
     phylo = Ponerinae_tree_old_calib,
     evolutionary_models = "DEC+J", # Default = "DEC" for biogeographic
     BioGeoBEARS_directory_path = tempdir(), # Ex: "./BioGeoBEARS_directory/"
     keep_BioGeoBEARS_files = FALSE,
     prefix_for_files = "Ponerinae_old_calib",
     max_range_size = 2,
     split_multi_area_ranges = TRUE, # Set to TRUE to display the two outputs
     nb_simulations = 100, # Reduce to save time (Default = '1000')
     colors_per_levels = colors_per_levels,
     return_model_selection_df = TRUE,
     verbose = TRUE) 

 # Load directly output
 data(Ponerinae_biogeo_data_old_calib, package = "deepSTRAPP")

 ## Explore output
 str(Ponerinae_biogeo_data_old_calib, 1)

 ## Set focal time to 10 Mya
 focal_time <- 10

  # (May take several minutes to run)
 ## Run deepSTRAPP on net diversification rates for focal time = 10 Mya.

 Ponerinae_deepSTRAPP_biogeo_old_calib_10My <- run_deepSTRAPP_for_focal_time(
    densityMaps = Ponerinae_biogeo_data_old_calib$densityMaps,
    ace = Ponerinae_biogeo_data_old_calib$ace,
    tip_data = Ponerinae_NO_tip_data,
    nb_simulations = 100,
    trait_data_type = "biogeographic",
    BAMM_object = Ponerinae_BAMM_object_old_calib,
    focal_time = focal_time,
    uncertainty_strategy = "paired",
    return_updated_Maps = TRUE,
    return_updated_BAMM_object = TRUE)

 ## Explore output
 str(Ponerinae_deepSTRAPP_biogeo_old_calib_10My, max.level = 1)

 ## Plot updated contMap vs. updated diversification rates
 plot_traits_vs_rates_on_phylogeny_for_focal_time(
    deepSTRAPP_outputs = Ponerinae_deepSTRAPP_biogeo_old_calib_10My,
    # Adjust colors on densityMaps
    colors_per_levels = c("N" = "dodgerblue2", "O" = "orange"),
    # Show legend and label on BAMM plot
    legend = TRUE, labels = TRUE,
    cex_pies = 0.2, # Adjust size of ACE pies on densityMaps
    cex = 0.7) # Adjust size of tip labels on BAMM plot
    # PDF_file_path = "Updated_maps_biogeo_old_calib_10My.pdf") 

 # ----- Example 3: With outputs over_time ----- #

 ## Load directly outputs from run_deepSTRAPP_over_time()
 Ponerinae_deepSTRAPP_biogeo_old_calib_0_40 <- readRDS(system.file("extdata",
    "Ponerinae_deepSTRAPP_biogeo_old_calib_0_40.rds", package = "deepSTRAPP"))
 ## This dataset is only available in development versions installed from GitHub.
 # It is not available in CRAN versions.
 # Use remotes::install_github(repo = "MaelDore/deepSTRAPP") to get the latest development version.

 ## Explore output
 str(Ponerinae_deepSTRAPP_biogeo_old_calib_0_40, max.level =  1)

 ## Plot updated contMap vs. updated diversification rates for focal_time = 40My
 plot_traits_vs_rates_on_phylogeny_for_focal_time(
    deepSTRAPP_outputs = Ponerinae_deepSTRAPP_biogeo_old_calib_0_40,
    focal_time = 40, # Select focal_time = 40My
    # Adjust colors on densityMaps
    colors_per_levels = c("N" = "dodgerblue2", "O" = "orange"),
    # Show legend and label on BAMM plot
    legend = TRUE, labels = TRUE,
    cex_pies = 0.2, # Adjust size of ACE pies on densityMaps
    cex = 0.7) # Adjust size of tip labels on BAMM plot
    # PDF_file_path = "Updated_maps_biogeo_old_calib_40My.pdf")
}