plot_multi_morphospace: Plot Multiple Morphopaces

Description

Plots multiple morphospaces up to a given number of ordination axes.

Usage

plot_multi_morphospace(
  pcoa_input,
  n_axes = 4,
  taxon_groups = NULL,
  plot_taxon_names = FALSE,
  plot_convex_hulls = FALSE,
  plot_internal_nodes = FALSE,
  plot_edges = TRUE,
  plot_root = TRUE,
  root_colour = "red",
  palette = "viridis",
  plot_group_legend = TRUE
)

Arguments

pcoa_input: The main input in the format outputted from ordinate_cladistic_matrix.
n_axes: An integer indicating the total number of axes to plot (should minimally be three).
taxon_groups: See plot_morphospace.
plot_taxon_names: See plot_morphospace.
plot_convex_hulls: See plot_morphospace.
plot_internal_nodes: See plot_morphospace.
plot_edges: See plot_morphospace.
plot_root: See plot_morphospace.
root_colour: See plot_morphospace.
palette: See plot_morphospace.
plot_group_legend: See plot_morphospace.

Author

Emma Sherratt emma.sherratt@gmail.com and Graeme T. Lloyd graemetlloyd@gmail.com

Details

Takes the output from ordinate_cladistic_matrix and uses plot_morphospace to plot the first N ordination axes.

This allows the user a better appreciation of how variance is distributed across multiple axes and all plots are scaled the saem way to further aid visualisation. Data will seem to "shrink" towards the centre of the space on higher axes as variance decreases.

Most of the options are simply passed to plot_morphospace, but the full range is not available as many will be inappropriate here (e.g., adding a z-axis).

Examples

Run this code


# Make PCoA for Day 2016 data set:
pcoa_input <- ordinate_cladistic_matrix(cladistic_matrix = day_2016)

# 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", "Lycaenodon_longiceps"),
   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 taxon groups including convex hulls:
plot_multi_morphospace(pcoa_input, n_axes = 5, taxon_groups = taxon_groups,
  plot_convex_hulls = TRUE)

# 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

# Make same plot as before but with a phylogeny:
plot_multi_morphospace(
  pcoa_input = pcoa_input,
  n_axes = 5,
  taxon_groups = taxon_groups,
  plot_convex_hulls = TRUE
)