plot.CanonicalDistanceAnalysis: Plots a Canonical Distance Analysis

View source: R/plot.CanonicalDistanceAnalysis.R

plot.CanonicalDistanceAnalysisR 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.

See Also

plot.Canonical.Biplot

Examples

# Not yet

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