Plot continuous trait evolution on the tree

Plot on a time-calibrated phylogeny the evolution of a continuous trait as summarized in a contMap object typically generated with prepare_trait_data().

This function is a wrapper of original functions from the R package {phytools}:

Step 1: Use phytools::setMap() to update the color scale if requested.
Step 2: Use phytools::plot.contMap() to plot the mapped phylogeny.

Usage

plot_contMap(
  contMap,
  ...,
  color_scale = NULL,
  display_plot = TRUE,
  PDF_file_path = NULL
)

Arguments

contMap: List of class "contMap", typically generated with prepare_trait_data(), that contains a phylogenetic tree and associated ancestral trait estimates mapped along branches in contMap$tree$maps.
...: Additional arguments to pass down to phytools::plot.contMap() to control 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. Default (color_scale = NULL) is using the color palette recorded in the contMap$cols item. If none was provided, the rainbow() palette is used. Provide the full argument name to avoid ambiguity with the col 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 plots the time-calibrated phylogeny displaying the evolution of a continuous trait. If PDF_file_path is provided, the function exports the plot into a PDF file.

An object of class "contMap" with an (optionally) updated color scale ($cols) is returned invisibly.

Details

This function is a wrapper of original functions phytools::setMap() and phytools::plot.contMap(). Additions are listed below:

The color scale can be controlled directly with the argument color_scale.
The plot can be exported in PDF using PDF_file_path to define the output file.

Author

Maël Doré

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

Examples

# Load phylogeny
data(Ponerinae_trait_tip_data, package = "deepSTRAPP")
# Load trait df
data(Ponerinae_tree, package = "deepSTRAPP")

## Prepare trait data

 # (May take several minutes to run)
# 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)

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

# Infer Ancestral Character Estimates based on a Brownian Motion model
# and run a Stochastic Mapping to interpolate values along branches and obtain a "contMap" object
Ponerinae_contMap <- phytools::contMap(Ponerinae_tree, x = Ponerinae_cont_tip_data,
                                       res = 100, # Number of time steps
                                       plot = FALSE)

# Plot contMap with the phytools method
plot(x = Ponerinae_contMap, fsize = c(0.5, 1))


# Plot contMap with an updated color scale
plot_contMap(contMap = Ponerinae_contMap, fsize = c(0.5, 1),
             color_scale = c("darkgreen", "limegreen", "orange", "red"))

             # PDF_file_path = "Ponerinae_contMap.pdf")