plot_multi_morphospace: Plot Multiple Morphopaces
In Claddis: Measuring Morphological Diversity and Evolutionary Tempo

Description Usage Arguments Details Author(s) See Also Examples

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

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
)

`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.

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).

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

assign_taxa_to_bins, plot_chronophylomorphospace, plot_morphospace_stack, plot_morphospace, ordinate_cladistic_matrix

# 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"))

# 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
)