Plot background 2D shape models

Plot the output from morphogrid(), for 2-dimensional morphometric data. Used internally.

plot_morphogrid2d(
  x = NULL,
  y = NULL,
  morphogrid,
  template = NULL,
  links = NULL,
  datype,
  ordtype,
  axes,
  adj_frame = c(1, 1),
  p,
  xlab = NULL,
  ylab = NULL,
  cex.ldm,
  col.ldm,
  col.models,
  lwd.models,
  bg.models,
  plot = TRUE,
  models = TRUE
)

Arguments

x

Optional vector with a non-morphometric variable to be plotted in the x axis.

y

Optional vector with a non-morphometric variable to be plotted in the y axis.

morphogrid

An object containing the output of morphogrid.

template

A 2-column matrix containing landmarks/semilandmarks followed by coordinates defining a curve or set of curves describing additional aspects of morphology, which will be warped using TPS interpolation to produce the set of background shell models (see build_template2d).

links

A list with the indices of the coordinates defining the wireframe (following the format used in Morpho).

datype

Character; type of shape data used ("landm" or "fcoef").

ordtype

Character; method used for multivariate ordination ("prcomp", "bg_prcomp", "phy_prcomp", "pls_shapes" or "phy_pls_shapes").

axes

Numeric of length 2, indicating the axes to be plotted.

adj_frame

Numeric of length 2, providing a posteriori scaling factors for the width and height of the frame, respectively.

p

Numeric, indicating the number of landmarks/semilandmarks used (for landmark data only).

xlab, ylab

Standard arguments passed to the generic plot function.

cex.ldm

Numeric; size of landmarks/semilandmarks in the background models.

col.ldm

The color of landmarks/semilandmarks in the background models.

col.models

The color for wireframes/outlines.

lwd.models

Numeric; the width of the lines in wireframes/outlines.

bg.models

Background color for outlines.

plot

Logical; whether to plot morphospace.

models

Logical; whether to plot background shape models.

See also

morphogrid, adjust_models2d

Examples

#load data and packages
library(geomorph)
data("tails")

#perform pca on tails shapes
pca <- prcomp(two.d.array(tails$shapes))

#generate grid of shape models sampling the range of variation
#at 4 locations (the 4 corners of the scatterplot)
shapes_grid <- morphogrid(ordination = pca, axes = c(1,2), datype = "landm",
                          k = ncol(tails$shapes), p = nrow(tails$shapes),
                          nh = 2, nv = 2)

#plot grid
plot_morphogrid2d(morphogrid = shapes_grid, links = tails$links,
                  datype = "landm", ordtype = "prcomp",
                  axes = c(1,2), p = 9, col.ldm = 1, cex.ldm = 1,
                  col.models = 1, lwd.models = 1)

#project each shape in models_arr
points(shapes_grid$models_arr[,,1], pch=16, col = 1)
points(shapes_grid$models_arr[,,2], pch=16, col = 2)
points(shapes_grid$models_arr[,,3], pch=16, col = 3)
points(shapes_grid$models_arr[,,4], pch=16, col = 4)