gg.shape.space: Shape space in the ggplot style

In aphanotus/borealis: Tools for reproducible geometric morphometric analysis

Shape space in the ggplot style

Description

Make pretty plots from geometric morphometric ordinations using the output of gm.prcomp (Adams et al. 2020).

Usage

gg.shape.space(
  x,
  axis1 = 1,
  axis2 = 2,
  main.title = NULL,
  group = NULL,
  group.title = NULL,
  convex.hulls = FALSE,
  label.groups = TRUE,
  labels = NULL,
  include.legend = FALSE,
  fixed.aspect = FALSE,
  xlim = NULL,
  ylim = NULL,
  color = NULL,
  pt.size = 1.5,
  pt.alpha = 0.85,
  hull.alpha = 0.2,
  save.as = NULL,
  height = 5,
  width = 7,
  scale = 1,
  units = "in",
  backtransform.examples = FALSE,
  shape.method = "points",
  lm.labels = TRUE,
  ref.shape = NULL,
  bt.links = NULL,
  bt.shape.mag = 1,
  bt.inset.size = 0.35,
  bt.margin.factor = 2,
  bt.legend.position = c(1, 1),
  ref.pt.size = 1,
  target.pt.size = 0.75,
  viridis.color.option = "viridis",
  group.label.size = 2.5,
  point.label.size = 2.5
)

Arguments

x	An object of class gm.prcomp.
axis1	The PC axis to plot on the horizontal.
axis2	The PC axis to plot on the vertical.
main.title	An optional title for the plot.
group	A factor to group samples.
group.title	An optional title for the group legend.
convex.hulls	A logical factor specifying whether to plot convex hulls around groups.
label.groups	A logical factor specifying whether to label groups.
labels	An optional character vector of point labels.
include.legend	A logical factor specifying whether to include a legend.
fixed.aspect	A logical factor specifying whether to use a fixed aspect ratio.
xlim	Set x scale limits
ylim	Set y scale limits
color	The color of points and hulls in each group.
pt.size	The size of individual points.
pt.alpha	The opacity of individual points.
hull.alpha	The opacity of the convex hulls.
save.as	An optional filename to export the plot.
height	The height of the exported plot.
width	The width of the exported plot.
scale	A scale factor for elements of the exported plot.
units	The units for height and width of the exported plot.
backtransform.examples	A logical factor specifying whether to include example shapes at the extremes of each axis.
shape.method	Method used to visualize shape differences, following geomorph::plotRefToTarget.
lm.labels	A logical factor specifying whether to label landmarks in the example shapes.
ref.shape	A reference of consensus shape.
bt.links	A matrix with two columns indicating landmarks to connect by lines in the example shapes.
bt.shape.mag	The desired magnification to be used on the example shape, in comparison to the reference.
bt.inset.size	The relative size of the example shape insets.
bt.margin.factor	A factor to control size of the margin where example shapes are plotted.
bt.legend.position	A two-element vector specifying the justification and position of the legend in a back-transform plot.
ref.pt.size	Scale factor for reference configuration points (single value or vector of values)
target.pt.size	Scale factor for target configuration points (single value or vector of values)
viridis.color.option	The color pallette to use from the viridis package.
group.label.size	Font size for group labels.
point.label.size	Font size for individual point labels.

Details

Beware that right now, the save.as feature only works with backtransform.examples = FALSE.

Source

Dave Angelini [e-mail] [aut, cre]

References

Geomorph: Software for geometric morphometric analyses. R package version 3.2.1. D.C. Adams and M.L. Collyer and A. Kaliontzopoulou. 2020. (Link)

Examples

library(geomorph)
data(plethodon)

# GPA
Y.gpa <- gpagen(plethodon$land)
# Create a gm.prcomp object
PCA <- gm.prcomp(Y.gpa$coords)

# Morphospace plots
gg.shape.space(PCA, group = plethodon$species, group.title = 'species')
gg.shape.space(PCA, group = plethodon$species, group.title = 'species', convex.hulls = TRUE)
gg.shape.space(PCA, group = plethodon$species, group.title = 'species', convex.hulls = TRUE,
          axis1 = 1, axis2 = 3)
gg.shape.space(PCA, group = plethodon$species, group.title = 'species', convex.hulls = TRUE,
          viridis.color.option = 'plasma')
gg.shape.space(PCA, group = plethodon$species, group.title = 'species', convex.hulls = TRUE,
          color = c("royalblue","gray40"))

# Labeling points
gg.shape.space(PCA, group = plethodon$species, group.title = 'species', convex.hulls = TRUE,
          labels = plethodon$site,
          group.label.size = 8, point.label.size = 2,
          color = c("royalblue","gray40"))

# Plots with example shapes
gg.shape.space(PCA, group = plethodon$species, group.title = 'species', convex.hulls = TRUE,
          backtransform.examples = TRUE,
          ref.shape = Y.gpa$consensus)

# Custom links on the example shapes
pletho.links <- matrix(c(4,5,5,6,6,7,7,8,8,9,9,10,10,11,2,4,12,2,3,5),
                       ncol = 2, byrow = TRUE)
gg.shape.space(PCA, group = plethodon$species, group.title = 'species', convex.hulls = TRUE,
          backtransform.examples = TRUE,
          ref.shape = Y.gpa$consensus,
          bt.links = pletho.links)

# No links on the example shapes
gg.shape.space(PCA, group = plethodon$species, group.title = 'species', convex.hulls = TRUE,
          backtransform.examples = TRUE,
          ref.shape = Y.gpa$consensus,
          bt.links = "none")

# Example shapes displaysed as thin-plate spline (TPS) warp grids
gg.shape.space(PCA, group = plethodon$species, group.title = 'species', convex.hulls = TRUE,
          backtransform.examples = TRUE,
          ref.shape = Y.gpa$consensus,
          shape.method = "TPS",
          lm.labels = FALSE)

aphanotus/borealis documentation built on Nov. 4, 2022, 8:44 p.m.