plot_morphospace: Plot Morphopace

In Claddis: Measuring Morphological Diversity and Evolutionary Tempo

Description

Plots a morphospace using the output from ordinate_cladistic_matrix.

Usage

plot_morphospace(
  pcoa_input,
  x_axis = 1,
  y_axis = 2,
  z_axis = NULL,
  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,
  group_legend_position = "top_right",
  plot_z_legend = TRUE,
  z_legend_position = "bottom_right",
  inform = TRUE,
  x_limits = NULL,
  y_limits = NULL
)

Arguments

pcoa_input	The main input in the format output from ordinate_cladistic_matrix.
x_axis	Which ordination axis to plot as the x-axis (defaults to 1).
y_axis	Which ordination axis to plot as the y-axis (defaults to 2).
z_axis	Which ordination axis to plot as the z-axis (defaults to NULL, i.e., is not plotted).
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_taxon_names	Logical indicating whether to plot the names of the taxa (defaults to FALSE).
plot_convex_hulls	Logical indicating whether to plot convex hulls around any taxon_groups (if used).
plot_internal_nodes	Logical indicating whether to plot the internal nodes of the tree (if included in pcoa_input) (defaults to FALSE).
plot_edges	Logical indicating whether to plot the branches of the tree (if included in pcoa_input) (defaults to TRUE).
plot_root	Logical indicating whether to plot the root separately (defaults to FALSE).
root_colour	If plotting the root separately (previous option) sets the root colour.
palette	The palette to use for plotting each element of taxon_groups. See palette.
plot_group_legend	Logical indicating whether to plot a legend for taxon_groups. (Default is TRUE.)
group_legend_position	Position to plot the group legend. Must be one of bottom_left, bottom_right, top_left, or top_right (the default).
plot_z_legend	Logical indicating whether to plot a legend for the z-axis. (Default is TRUE.)
z_legend_position	Position to plot the group legend. Must be one of bottom_left, bottom_right (the default), top_left, or top_right.
inform	Logical indicating whether to inform the user of any taxon pruning. (Default is TRUE.)
x_limits	Plot limits to use for x-axis. Only intended for use by plot_multi_morphospace.
y_limits	Plot limits to use for y-axis. Only intended for use by plot_multi_morphospace.

Details

Uses output from ordinate_cladistic_matrix to make morphospace plots.

Allows plotting of a third axis using the technique of Wills et al. (1994; their Figures 4 and 8; Wills 1998; his Figure 4), where solid and open indicate positive and negative values respectively, and the size of points their magnitudes.

Will automatically generate phylomorphospaces if a tree was included in the ordination.

Can also plot groups of points - whether they represent taxonomic, ecological, temporal, or spatial groupings - in different colours as well as plot translucent convex hulls around these groups, by using the taxon_groups and plot_convex_hulls = TRUE options, respectively. Note that taxon_groups should be in the form of a named list (see example below for how these should be formatted).

Various other options allow toggling of particular features on or off. For example, the taxon names can be shown with plot_taxon_names = TRUE.

Note that some features will generate legends that may initially appear to disappear off the sides of the plot, but simple resizing of the plot window (or increasing the width:height ratio if outputting to a file) should fix this.

Author(s)

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

References

Wills, M. A., 1998. Cambrian and Recent disparity: the picture from priapulids. Paleobiology, 24, 177-199.

Wills, M. A., Briggs, D. E. G. and Fortey, R. A., 1994. Disparity as an evolutionary index: a comparison of Cambrian and Recent arthropods. Paleobiology, 20, 93-130.

See Also

assign_taxa_to_bins, plot_chronophylomorphospace, plot_morphospace_stack, plot_multi_morphospace, ordinate_cladistic_matrix

Examples

# Perform a PCoA ordination on the day_2016 data set:
pcoa_input <- ordinate_cladistic_matrix(cladistic_matrix = day_2016)

# Plot this as a simple bivarate morphospace:
plot_morphospace(pcoa_input = pcoa_input)

# Use the Wills technique to add a third axis (PC3):
plot_morphospace(pcoa_input = pcoa_input, z_axis = 3)

# You may need to resize the plot to see the legend for the z-axis

# Add taxon names as well:
plot_morphospace(pcoa_input = pcoa_input, z_axis = 3, plot_taxon_names = TRUE)

# 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",
  "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 taxon groups including convex hulls:
plot_morphospace(pcoa_input = pcoa_input, z_axis = 3, plot_taxon_names = TRUE,
  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

# 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"))

# Note: the above pruning is simply to run this example and should not be
# done manually as a matter of course as the functions will automatically
# prune tips and nodes as required.

# Make new ordination with tree included (enabling phylomorphospace):
pcoa_input <- ordinate_cladistic_matrix(cladistic_matrix = cladistic_matrix,
  time_tree = time_tree)

# Plot this as a simple bivarate phylomorphospace:
plot_morphospace(pcoa_input = pcoa_input)

# Use the Wills technique to add a third axis (PC3):
plot_morphospace(pcoa_input = pcoa_input, z_axis = 3)

# You may need to resize the plot to see the legend for the z-axis

# Add taxon names as well:
plot_morphospace(pcoa_input = pcoa_input, z_axis = 3, plot_taxon_names = TRUE)

# Add taxon groups including convex hulls:
plot_morphospace(pcoa_input = pcoa_input, z_axis = 3, plot_taxon_names = TRUE,
  taxon_groups = taxon_groups, plot_convex_hulls = TRUE)

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