R: Plot Function for RRPP

add.trajectories {RRPP}

R Documentation

Plot Function for RRPP

Description

Function adds trajectories to a principal component plot

Usage

add.trajectories(
  TP,
  traj.pch = 21,
  traj.col = 1,
  traj.lty = 1,
  traj.lwd = 1,
  traj.cex = 1.5,
  traj.bg = 1,
  start.bg = 3,
  end.bg = 2
)

Arguments

`TP`	plot object (from `plot.trajectory.analysis`)
`traj.pch`	Plotting "character" for trajectory points. Can be a single value or vector of length equal to the number of trajectories. See `par` and its description for pch.
`traj.col`	The color of trajectory lines. Can be a single value or vector of length equal to the number of trajectories. See `par` and its description for col.
`traj.lty`	Trajectory line type. Can be a single value or vector of length equal to the number of trajectories. See `par` and its description for lty.
`traj.lwd`	Trajectory line width. Can be a single value or vector of length equal to the number of trajectories. See `par` and its description for lwd.
`traj.cex`	Trajectory point character expansion. Can be a single value or vector of length equal to the number of trajectories. See `par` and its description for cex.
`traj.bg`	Trajectory point background. Can be a single value or vector of length equal to the number of trajectories. See `par` and its description for bg.
`start.bg`	Trajectory point background, just the start points. Can be a single value or vector of length equal to the number of trajectories. See `par` and its description for bg. Green start points are the default.
`end.bg`	Trajectory point background, just the end points. Can be a single value or vector of length equal to the number of trajectories. See `par` and its description for bg. Red end points are the default.

Details

The function adds trajectories to a plot made by plot.trajectory.analysis. This function has a restricted set of plot parameters based on the number of trajectories to be added to the plot.

Author(s)

Michael Collyer

References

Adams, D. C., and M. M. Cerney. 2007. Quantifying biomechanical motion using Procrustes motion analysis. J. Biomech. 40:437-444.

Adams, D. C., and M. L. Collyer. 2007. The analysis of character divergence along environmental gradients and other covariates. Evolution 61:510-515.

Adams, D. C., and M. L. Collyer. 2009. A general framework for the analysis of phenotypic trajectories in evolutionary studies. Evolution 63:1143-1154.

Collyer, M. L., and D. C. Adams. 2007. Analysis of two-state multivariate phenotypic change in ecological studies. Ecology 88:683-692.

Collyer, M. L., and D. C. Adams. 2013. Phenotypic trajectory analysis: comparison of shape change patterns in evolution and ecology. Hystrix 24: 75-83.

Collyer, M.L., D.J. Sekora, and D.C. Adams. 2015. A method for analysis of phenotypic change for phenotypes described by high-dimensional data. Heredity. 115:357-365.