plot_multi_morphospace {Claddis}

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.

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).

Author(s)

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

See Also

assign_taxa_to_bins, plot_chronophylomorphospace, plot_morphospace_stack, plot_morphospace, ordinate_cladistic_matrix

Examples

# 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
)