scree.plot: Plot the proportion of variance captured by each component...
In aphanotus/borealis: Tools for reproducible geometric morphometric analysis

scree.plot

R Documentation

Plot the proportion of variance captured by each component axis of a gm.prcomp object

Description

Plot the proportion of variance captured by each component axis of a gm.prcomp object

Usage

scree.plot(
  x,
  npcs = NULL,
  threshold = 0.05,
  threshold.color = "darkred",
  method = "percent",
  type = "barplot",
  ...
)

Arguments

`x`	An object of class `gm.prcomp`.
`npcs`	The number of components to be plotted.
`threshold`	An optional threshold to display. Default is 0.05.
`threshold.color`	Color for the threshold line.
`method`	A string indicating how to represent the proportion of variance. Allowable values are `"variance"`, `"proportion"`, and `"percentage"`. May be abbreviated.
`type`	A string indicating the type of plot. Options are `"barplot"` and `"lines"`. May be abbreviated.

Source

Dave Angelini david.r.angelini@gmail.com [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)

# scree plot
scree.plot(PCA)

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