PLOT.RDA: Plot the results of a redundancy analysis

In easyCODA: Compositional Data Analysis in Practice

Description

Various maps and biplots/triplots of the results of a redundancy analysis using function RDA.

Usage

PLOT.RDA(obj, map="symmetric", indcat=NA, rescale=1, dim=c(1,2), axes.inv=c(1,1),
         main="", rowstyle=1, cols=c("blue","red","forestgreen"),
         colarrows=c("pink","lightgreen"), colrows=NA, pchrows=NA, colcats=NA,
         cexs=c(0.8,0.8,0.8), fonts=c(2,4,4))

Arguments

obj	An RDA object created using function RDA
map	Choice of scaling of rows and columns: "symmetric" (default), "asymmetric" or "contribution"
indcat	A vector indicating which of the covariates are dummy (or fuzzy) variables
rescale	A rescaling factor applied to column coordinates(default is 1 for no rescaling). If rescale is a vector with two values, the first applies to the column coordinates and the second to the covariate coordinates.
dim	Dimensions selected for horizontal and vertical axes of the plot (default is c(1,2))
axes.inv	Option for reversing directions of horizontal and vertical axes (default is c(1,1) for no reversing, change one or both to -1 for reversing)
main	Title for plot
rowstyle	Scaling option for row coordinates, either 1 (SVD coordinates, default) or 2 (as supplementary points)
cols	Colours for row and column and covariate labels (default is c("blue","red","forestgreen"))
colarrows	Colour for arrows in asymmetric or contribution biplots, for columns and covariates (default is c("pink","lightgreen"))
colrows	Optional vector of colours for rows
pchrows	Optional vector of point symbols for rows
colcats	Optional vector of colours for covariate categories (dummy variables)
cexs	Vector of character expansion factors for row and column and covariate labels (default is c(0.8,0.8,0.8))
fonts	Vector of font styles for row and column and covariate labels (default is c(2,4,4))

Details

The function PLOT.RDA makes a scatterplot of the results of a redundancy analysis (computed using function RDA), with various options for scaling the results and changing the direction of the axes. By default, dimensions 1 and 2 are plotted on the horizontal and vertical axes, and it is assumed that row points refer to samples and columns to compositional parts. Covariates are plotted according to their regression coefficients with the RDA dimensions, and if they contain dummy (or fuzzy) variables these are indicated by the option indcat, and hence plotted as centroids not arrows.

By default, the symmetric scaling is used, where both rows and columns are in principal coordinates and have the same amount of weighted variance along the two dimensions. The other options are the asymmetric option, when columns are in standard coordinates, and the contribution option, when columns are in contribution coordinates. In cases where the row and column displays as well as the covariate positions occupy widely different extents, the column and covariate coordinates can be rescaled using the rescale option.

Author(s)

Michael Greenacre

See Also

RDA

Examples

# see the use of PLOT.RDA in the example of the RDA function

Example output

Loading required package: ca
Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-7
Loading required package: ellipse

Attaching package: ‘ellipse’

The following object is masked from ‘package:graphics’:

    pairs

easyCODA documentation built on Sept. 20, 2020, 1:07 a.m.