plot_chronophylomorphospace: Chronophylomorphospace Plot

In Claddis: Measuring Morphological Diversity and Evolutionary Tempo

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	A named list of groups to which taxa are assigned (optional). This is used to plot points or convex hulls in different colours corresponding to each group. As the user names the groups these can represent any grouping of interest (e.g., taxonomic, ecological, temporal, spatial). assign_taxa_to_bins can automate temporal assignments.
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"))

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

## End(Not run)

Claddis documentation built on Oct. 23, 2020, 8:04 p.m.