Plots the solution of a Canonical Correspondence Analysisis using similar parameters to the continuous biplot
# S3 method for 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, ...)No value returned
The results of a CCA model
Dimension for the first axis
Dimension for the second axis
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 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.
Should the sites be plotted?
Should the species be plotted?
Should the environmental variables be plotted?
Labels for the sites
Labels for the species
Labels for the environmental variables.
Type for the sites plot
Quality for the species
Minimum quality to plot a variable
A set of indices with the variables that will show the projections of the individuals.
A set of indices with the individuals to show the projections on the variables.
Should the axis be plotted?
Type of scale to use : "Complete", "StdDev" or "BoxPlot"
Values to show on the scale: "Original" or "Transformed"
Mode of the biplot: "p", "a", "b", "h", "ah" and "s".
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.
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.
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.
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.
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.
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.
Symbol for the sites points. See help(points) for details.
Symbol for the species points. See help(points) for details.
Symbol for the variables points. See help(points) for details.
Should the size of the site points be related to their qualities of representation (predictiveness)?
Should the size of the species points be related to their qualities of representation (predictiveness)?
Should the size of the variables points be related to their qualities of representation (predictiveness)?
Should the color of the sites points be related to their qualities of representation (predictiveness)?
Should the color of the species points be related to their qualities of representation (predictiveness)?
Should the color of the variables points be related to their qualities of representation (predictiveness)?
Plot the labels in a smart way
Aditional graphical parameters.
Jose Luis Vicente Villardon
The plotting procedure is similar to the one used for continuous biplots including the calibration of the environmental variables.
CCA
plot.ContinuousBiplot
##---- Should be DIRECTLY executable !! ----
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