geomorph: plot.gm.prcomp – R documentation

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geomorph

plot.gm.prcomp

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 = 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)),
  ...
)

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