plot_chronophylomorphospace: Chronophylomorphospace Plot

In graemetlloyd/Claddis: Measuring Morphological Diversity and Evolutionary Tempo

Chronophylomorphospace Plot

Description

Plots a three-dimensional chronophylomorphospace.

Usage

plot_chronophylomorphospace(
  pcoa_input,
  x_axis = 1,
  y_axis = 2,
  taxon_groups = NULL,
  plot_tips = TRUE,
  plot_nodes = TRUE,
  plot_taxon_names = TRUE,
  plot_edges = TRUE,
  shadow = TRUE,
  plot_group_legend = TRUE,
  group_legend_position = "top_right",
  palette = "viridis"
)

Arguments

pcoa_input	Principal coordinate data in the format output by ordinate_cladistic_matrix that includes a tree and ancestral states.
x_axis	Which ordination axis to plot as the x-axis.
y_axis	Which ordination axis to plot as the y-axis.
taxon_groups	An object of class taxonGroups.
plot_tips	Whether or not to plot the tip nodes (defaults to TRUE).
plot_nodes	Whether or not to plot the internal nodes (defaults to TRUE).
plot_taxon_names	Whether or not to show the taxon nodes (defaults to TRUE).
plot_edges	Whether or not to plot the branches (defaults to TRUE).
shadow	Whether or not to plot a shadow (2D plot) on the bottom face of the 3D plot (defaults to TRUE).
plot_group_legend	Whether or not to add a legend to identify the groups. Only relevant if using "taxon_groups".
group_legend_position	Position to plot the group legend. Must be one of bottom_left, bottom_right, top_left, or top_right (the default).
palette	The palette to use for plotting each element of taxon_groups. See palette.

Details

Creates a manually repositionable three-dimensional (two ordination axes plus time) plot of a phylomorphospace.

This function aims to mimic the data visualisation of Sakamoto and Ruta (2012; their Video S1).

Author(s)

Emma Sherratt [e-mail] and Graeme T. Lloyd [e-mail]

References

Sakamoto, M. and Ruta, M. 2012. Convergence and divergence in the evolution of cat skulls: temporal and spatial patterns of morphological diversity. PLoS ONE, 7, e39752.

See Also

assign_taxa_to_bins, plot_morphospace_stack, plot_morphospace, plot_multi_morphospace, ordinate_cladistic_matrix

Examples

## Not run: 
# Require rgl library to use:
require(rgl)

# Make time-scaled first MPT for Day 2016 data set:
time_tree <- ape::read.tree(text = paste0("(Biarmosuchus_tener:0.5,",
  "(((Hipposaurus_boonstrai:3.5,(Bullacephalus_jacksoni:0.75,",
  "Pachydectes_elsi:0.75):0.75):0.75,(Lemurosaurus_pricei:7.166666667,",
  "(Lobalopex_mordax:4.333333333,((Lophorhinus_willodenensis:3.666666667,",
  "(Proburnetia_viatkensis:0.8333333333,(Lende_chiweta:2,",
  "(Paraburnetia_sneeubergensis:1,Burnetia_mirabilis:2):1):1.833333333)",
  ":0.8333333333):0.8333333333,(BP_1_7098:2.25,Niuksenitia_sukhonensis:",
  "1.25):1.25):0.8333333333):0.8333333333):3.083333333):1.95,",
  "(Ictidorhinus_martinsi:15.9,(RC_20:11.6,(Herpetoskylax_hopsoni:11.3,",
  "Lycaenodon_longiceps:0.3):0.3):0.3):0.3):0.3);"))

# Add root age to tree:
time_tree$root.time <- 269.5

# Prune incomplete taxa from tree:
time_tree <- ape::drop.tip(phy = time_tree, tip = c("Lycaenodon_longiceps",
  "Niuksenitia_sukhonensis"))

# Prune incomplete taxa from cladistic matrix:
cladistic_matrix <- prune_cladistic_matrix(cladistic_matrix = day_2016,
  taxa2prune = c("Lycaenodon_longiceps", "Niuksenitia_sukhonensis"))

# Perform a phylogenetic Principal Coordinates Analysis:
pcoa_input <- ordinate_cladistic_matrix(
  cladistic_matrix = cladistic_matrix,
  time_tree = time_tree
)

# Define some simple taxon groups for the data as a named list:
taxon_groups <- list(nonBurnetiamorpha = c("Biarmosuchus_tener",
  "Hipposaurus_boonstrai", "Bullacephalus_jacksoni", "Pachydectes_elsi",
  "Niuksenitia_sukhonensis", "Ictidorhinus_martinsi", "RC_20",
  "Herpetoskylax_hopsoni"),
  Burnetiamorpha = c("Lemurosaurus_pricei", "Lobalopex_mordax",
  "Lophorhinus_willodenensis", "Proburnetia_viatkensis", "Lende_chiweta",
  "Paraburnetia_sneeubergensis", "Burnetia_mirabilis", "BP_1_7098"))

# Set class as taxonGroups:
class(taxon_groups) <- "taxonGroups"

# Plot a chronophylomorphospace:
plot_chronophylomorphospace(
  pcoa_input = pcoa_input,
  taxon_groups = taxon_groups,
)

## End(Not run)

graemetlloyd/Claddis documentation built on Sept. 8, 2024, 12:51 p.m.