PLOT.RDA {easyCODA}

Plot the results of a redundancy analysis

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