plot.gm.prcomp: Plot Function for geomorph

In geomorphR/geomorph: Geometric Morphometric Analyses of 2D and 3D Landmark Data

Plot Function for geomorph

Description

Plot Function for geomorph

Usage

## S3 method for class 'gm.prcomp'
plot(
  x,
  axis1 = 1,
  axis2 = 2,
  flip = NULL,
  phylo = FALSE,
  time.plot = FALSE,
  phylo.par = NULL,
  ...
)

Arguments

x	An object of class gm.prcomp
axis1	A value indicating which PC axis should be displayed as the X-axis (default = PC1)
axis2	A value indicating which PC axis should be displayed as the Y-axis (default = PC2)
flip	An argument that if not NULL can be used to flip components in the plot. The values need to match axis1 or axis2. For example, if axis1 = 3 and axis2 = 4, flip = 1 will not change either axis; flip = 3 will flip only the horizontal axis; flip = c(3, 4) will flip both axes.
phylo	A logical value indicating whether the phylogeny should be projected to PC space
time.plot	A logical value indicating if a 3D plot with the phylogeny and time as the z-axis is desired
phylo.par	A list of plotting parameters for the inclusion of a phylogeny, including: logicals for whether features should be included (tip.labels, nodel.labels, anc.states), toggled as TRUE/FALSE; edge parameters (edge.color, edge.width, edge.lty); node parameters (node.bg, node.pch, node.cex); and label parameters (tip.txt.cex, tip.txt.col, tip.txt.adj, node.txt.cex, node.txt.col, node.txt.adj).
...	other arguments passed to plot. For plots with a phylogeny, these parameters pertain to the tip values.

Value

An object of class "plot.gm.prcomp" is a list with components that can be used in other plot functions, such as the type of plot, points, a group factor, and other information depending on the plot parameters used. A time plot is an addendum to the normal 2D plot, and does not add additional output.

NOTE: To visualize shape variation across PC axes in 2d plots, use picknplot.shape.

Author(s)

Antigoni Kaliontzopoulou, Michael Collyer

See Also

plotRefToTarget picknplot.shape

geomorphR/geomorph documentation built on June 12, 2025, 8:35 p.m.