plot.CCA.sol {MultBiplotR}

Plots the solution of a Canonical Correspondence Analysisis

Description

Plots the solution of a Canonical Correspondence Analysisis using similar parameters to the continuous biplot

Usage

## S3 method for class 'CCA.sol'
plot(x, A1 = 1, A2 = 2, ShowAxis = FALSE, margin = 0,
                 PlotSites = TRUE, PlotSpecies = TRUE, PlotEnv = TRUE,
                 LabelSites = TRUE, LabelSpecies = TRUE, LabelEnv =
                 TRUE, TypeSites = "wa", SpeciesQuality = FALSE,
                 MinQualityVars = 0.3, dp = 0, pr = 0, PlotAxis =
                 FALSE, TypeScale = "Complete", ValuesScale =
                 "Original", mode = "a", CexSites = NULL, CexSpecies =
                 NULL, CexVar = NULL, ColorSites = NULL, ColorSpecies =
                 NULL, ColorVar = NULL, PchSites = NULL, PchSpecies =
                 NULL, PchVar = NULL, SizeQualSites = FALSE,
                 SizeQualSpecies = FALSE, SizeQualVars = FALSE,
                 ColorQualSites = FALSE, ColorQualSpecies = FALSE,
                 ColorQualVars = FALSE, SmartLabels = FALSE, ...)

Arguments

x

The results of a CCA model

A1

Dimension for the first axis

A2

Dimension for the second axis

ShowAxis

Logical variable to control if the coordinate axes should appear in the plot. The default value is FALSE because for most of the biplots its presence is irrelevant.

margin

Margin for the labels in some of the biplot modes (percentage of the plot width). Default is 0. Increase the value if the labels are not completely plotted.

PlotSites

Should the sites be plotted?

PlotSpecies

Should the species be plotted?

PlotEnv

Should the environmental variables be plotted?

LabelSites

Labels for the sites

LabelSpecies

Labels for the species

LabelEnv

Labels for the environmental variables.

TypeSites

Type for the sites plot

SpeciesQuality

Quality for the species

MinQualityVars

Minimum quality to plot a variable

dp

A set of indices with the variables that will show the projections of the individuals.

pr

A set of indices with the individuals to show the projections on the variables.

PlotAxis

Should the axis be plotted?

TypeScale

Type of scale to use : "Complete", "StdDev" or "BoxPlot"

ValuesScale

Values to show on the scale: "Original" or "Transformed"

mode

Mode of the biplot: "p", "a", "b", "h", "ah" and "s".

CexSites

Size for the symbols and labels of the sites. Can be a single common size for all the points or a vector with individual sizes.

CexSpecies

Size for the symbols and labels of the species. Can be a single common size for all the points or a vector with individual sizes.

CexVar

Size for the symbols and labels of the variables. Can be a single common size for all the points or a vector with individual sizes.

ColorSites

Color for the symbols and labels of the sites. Can be a single common color for all the points or a vector with individual colors.

ColorSpecies

Color for the symbols and labels of the species. Can be a single common color for all the points or a vector with individual colors.

ColorVar

Color for the symbols and labels of the variables. Can be a single common color for all the points or a vector with individual colors.

PchSites

Symbol for the sites points. See help(points) for details.

PchSpecies

Symbol for the species points. See help(points) for details.

PchVar

Symbol for the variables points. See help(points) for details.

SizeQualSites

Should the size of the site points be related to their qualities of representation (predictiveness)?

SizeQualSpecies

Should the size of the species points be related to their qualities of representation (predictiveness)?

SizeQualVars

Should the size of the variables points be related to their qualities of representation (predictiveness)?

ColorQualSites

Should the color of the sites points be related to their qualities of representation (predictiveness)?

ColorQualSpecies

Should the color of the species points be related to their qualities of representation (predictiveness)?

ColorQualVars

Should the color of the variables points be related to their qualities of representation (predictiveness)?

SmartLabels

Plot the labels in a smart way

...

Aditional graphical parameters.

Details

The plotting procedure is similar to the one used for continuous biplots including the calibration of the environmental variables.

Value

No value returned

Author(s)

Jose Luis Vicente Villardon

References

CCA

See Also

plot.ContinuousBiplot

Examples

##---- Should be DIRECTLY executable !! ----