Plot Function for geomorph
# S3 method for gm.prcomp
plot(
x,
axis1 = 1,
axis2 = 2,
flip = NULL,
phylo = FALSE,
time.plot = FALSE,
phylo.par = list(tip.labels = TRUE, node.labels = TRUE, anc.states = TRUE, node.pch =
21, node.bg = "grey", node.cex = 1, edge.color = "black", edge.width = 1, tip.txt.cex
= 1, tip.txt.col = "black", tip.txt.adj = c(-0.1, -0.1), node.txt.cex = 1,
node.txt.col = "grey", node.txt.adj = c(-0.1, -0.1)),
...
)An object of class gm.prcomp
A value indicating which PC axis should be displayed as the X-axis (default = PC1)
A value indicating which PC axis should be displayed as the Y-axis (default = PC2)
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.
A logical value indicating whether the phylogeny should be projected to PC space
A logical value indicating if a 3D plot with the phylogeny and time as the z-axis is desired
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.
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.