plot.CCA.sol: Plots the solution of a Canonical Correspondence Analysisis

In MultBiplotR: Multivariate Analysis Using Biplots in R

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 !! ----

MultBiplotR documentation built on Nov. 21, 2023, 5:08 p.m.