Plots a Canonical Distance Analysis
# S3 method for CanonicalDistanceAnalysis
plot(x, A1 = 1, A2 = 2, ScaleGraph = TRUE,
ShowAxis = FALSE, ShowAxes = FALSE, LabelAxes = TRUE, margin = 0.1,
PlotAxis = FALSE, ShowBox = TRUE, PlotGroups = TRUE, LabelGroups = TRUE,
CexGroup = 1.5, PchGroup = 16, ColorGroup = NULL, voronoi = TRUE,
VoronoiColor = "black", PlotInd = TRUE, LabelInd = TRUE, CexInd = 0.8,
PchInd = 3, ColorInd = NULL, WhatInds = NULL, IndLabels = NULL,
PlotVars = TRUE, LabelVar = TRUE, CexVar = NULL, PchVar = NULL,
ColorVar = NULL, WhatVars = NULL, VarLabels = NULL, mode = "a",
TypeScale = "Complete", ValuesScale = "Original", SmartLabels = TRUE,
AddLegend = TRUE, LegendPos = "topright", PlotCircle = TRUE,
ConvexHulls = FALSE, TypeCircle = "M", MinQualityVars = 0, dpg = 0,
dpi = 0, PredPoints = 0, PlotClus = TRUE, TypeClus = "ch", ClustConf = 1,
CexClustCenters = 1, ClustCenters = FALSE, UseClusterColors = TRUE, ...)The plot of a Canonical Distance Analysis
An object of class "CanonicalDistanceAnalysis"
Dimension for the first axis. 1 is the default.
Dimension for the second axis. 2 is the default.
Reescale the coordinates to optimal matching.
Should the axis be shown?
Not used
Shoud the axis be labelled?
Margin of the plot
Should the axis be plotted?
Show a box around the plot
Should the groups be plotted?
Should the groups be labelled?
Sizes for the groups
Marks for the groups
Colors for the groups
Should a voronoi diagram separating the groups be plotted?
Color for the voronoi diagram
Should the individuals be plotted?
Should the individuals be labelled?
Sizes for the individuals
Marks for the individuals
Colors for the individuals
What indivduals are plotted
Labels for the individuals
Should the variables be plotted?
Should the variables be labelled?
Sizes for the variables
Marks for the variables
User colors for the variables. Default colors will be used if NULL.
What Variables are plotted
User labels for the variables
Mode of the biplot: "p", "a", "b", "h", "ah" and "s".
Type of scale to use : "Complete", "StdDev" or "BoxPlot"
Values to show on the scale: "Original" or "Transformed"
Plot the labels in a smart way
Should a legend be added?
Position of the legend
Should the confidence regions for the groups be plotted?
Should the convex hulls containing the individuals for each group be plotted?
Type of confidence region: Univariate (U), Bonferroni(B), Multivariate (M) or Classical (C)
Minimum quality of representation for a variable to be plotted
A set of indices with the variables that will show the projections of the gorups
A set of indices with the individuasl that will show the projections on the variables
A vector with integers. The group centers listed in the vector are projected onto all the variables.
Should the clusters be plotted?
Type of plot for the clusters. ("ch"- Convex Hull, "el"- Ellipse or "st"- Star)
Percent of points included in the cluster. only the ClusConf percent of the points nearest to the center will be used to calculate the cluster
SIze of the cluster centers.
Should the cluster centers be plotted?
Should the cluster colors be used in the plot
Any other graphical parameters
Jose Luis Vicente Villardon
Plots a Canonical Distance Analysis
Gower, J. C. and Krzanowski, W. J. (1999). Analysis of distance for structured multivariate data and extensions to multivariate analysis of variance. Journal of the Royal Statistical Society: Series C (Applied Statistics), 48(4):505-519.
plot.Canonical.Biplot