plot.CanonicalDistanceAnalysis: Plots a Canonical Distance Analysis
In MultBiplotR: Multivariate Analysis Using Biplots in R

View source: R/plot.CanonicalDistanceAnalysis.R

plot.CanonicalDistanceAnalysis

R Documentation

Plots a Canonical Distance Analysis

Description

Plots a Canonical Distance Analysis

Usage

## S3 method for class '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, ...)

Arguments

`x`	An object of class "CanonicalDistanceAnalysis"
`A1`	Dimension for the first axis. 1 is the default.
`A2`	Dimension for the second axis. 2 is the default.
`ScaleGraph`	Reescale the coordinates to optimal matching.
`ShowAxis`	Should the axis be shown?
`ShowAxes`	Not used
`LabelAxes`	Shoud the axis be labelled?
`margin`	Margin of the plot
`PlotAxis`	Should the axis be plotted?
`ShowBox`	Show a box around the plot
`PlotGroups`	Should the groups be plotted?
`LabelGroups`	Should the groups be labelled?
`CexGroup`	Sizes for the groups
`PchGroup`	Marks for the groups
`ColorGroup`	Colors for the groups
`voronoi`	Should a voronoi diagram separating the groups be plotted?
`VoronoiColor`	Color for the voronoi diagram
`PlotInd`	Should the individuals be plotted?
`LabelInd`	Should the individuals be labelled?
`CexInd`	Sizes for the individuals
`PchInd`	Marks for the individuals
`ColorInd`	Colors for the individuals
`WhatInds`	What indivduals are plotted
`IndLabels`	Labels for the individuals
`PlotVars`	Should the variables be plotted?
`LabelVar`	Should the variables be labelled?
`CexVar`	Sizes for the variables
`PchVar`	Marks for the variables
`ColorVar`	User colors for the variables. Default colors will be used if NULL.
`WhatVars`	What Variables are plotted
`VarLabels`	User labels for the variables
`mode`	Mode of the biplot: "p", "a", "b", "h", "ah" and "s".
`TypeScale`	Type of scale to use : "Complete", "StdDev" or "BoxPlot"
`ValuesScale`	Values to show on the scale: "Original" or "Transformed"
`SmartLabels`	Plot the labels in a smart way
`AddLegend`	Should a legend be added?
`LegendPos`	Position of the legend
`PlotCircle`	Should the confidence regions for the groups be plotted?
`ConvexHulls`	Should the convex hulls containing the individuals for each group be plotted?
`TypeCircle`	Type of confidence region: Univariate (U), Bonferroni(B), Multivariate (M) or Classical (C)
`MinQualityVars`	Minimum quality of representation for a variable to be plotted
`dpg`	A set of indices with the variables that will show the projections of the gorups
`dpi`	A set of indices with the individuasl that will show the projections on the variables
`PredPoints`	A vector with integers. The group centers listed in the vector are projected onto all the variables.
`PlotClus`	Should the clusters be plotted?
`TypeClus`	Type of plot for the clusters. ("ch"- Convex Hull, "el"- Ellipse or "st"- Star)
`ClustConf`	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
`CexClustCenters`	SIze of the cluster centers.
`ClustCenters`	Should the cluster centers be plotted?
`UseClusterColors`	Should the cluster colors be used in the plot
`...`	Any other graphical parameters

Details

Plots a Canonical Distance Analysis

Value

The plot of a Canonical Distance Analysis

Author(s)

Jose Luis Vicente Villardon

References

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.