plot.Principal.Coordinates: Plots an object of class Principal.Coordinates

In MultBiplotR: Multivariate Analysis Using Biplots in R

Plots an object of class Principal.Coordinates

Description

Plots an object of class Principal.Coordinates

Usage

## S3 method for class 'Principal.Coordinates'
plot(x, A1 = 1, A2 = 2, LabelRows = TRUE, 
WhatRows = NULL, RowCex = 1, RowPch = 16, Title = "", RowLabels = NULL, 
RowColors = NULL, ColColors = NULL, ColLabels = NULL, SizeQualInd = FALSE, 
SmartLabels = TRUE, ColorQualInd = FALSE, ColorQual = "black", PlotSup = TRUE, 
Bootstrap = FALSE, BootstrapPlot = c("Ellipse", "CovexHull", "Star"), 
margin = 0, PlotClus = FALSE, TypeClus = "ch", ClustConf = 1, 
CexClustCenters = 1, LegendClust = TRUE, ClustCenters = FALSE, 
UseClusterColors = TRUE, ShowAxis = FALSE, PlotBinaryMeans = FALSE, 
MinIncidence = 0, ShowBox = FALSE, ColorSupContVars = NULL, 
ColorSupBinVars = NULL, ColorSupOrdVars = NULL, TypeScale = "Complete", 
SupMode = "s", PlotSupVars = FALSE, ...)

Arguments

x	Object of class "Principal.Coordinates"
A1	First dimenssion of the plot
A2	Second dimenssion of the plot
LabelRows	Controls if the points are labelled. Usually TRUE.
WhatRows	What Rows to plot. A vector of 0/1 elements. If NULL all rows are plotted
RowCex	Size of the points. Can be a single number or a vector.
RowPch	Symbols for the points.
Title	Title for the graph
RowLabels	Labels for the rows. If NULL row names of the data matrix are used.
RowColors	Colors for the rows. If NULL row deafault colors are assigned. Can be a single value or avector of colors.
ColColors	Colors for the columns (Variables)
ColLabels	Labels for the columns (Variables)
SizeQualInd	Controls if the size of points depends on the quality of representation.
SmartLabels	Controls the way labels are plotted on the graph. If TRUE labels for points with positive x values are placed to the right of the point and labels for points with negative values to the left
ColorQualInd	Controls if the color of the points depends on the quality of representation.
ColorQual	Darker color for the quality scale.
PlotSup	Controls if the supplementary points are plotted.
Bootstrap	Controls if the bootstrap points are plotted.
BootstrapPlot	Type of plot of the Bootstrap Information. The types are "Ellipse", "CovexHull" or "Star".
margin	Margin for the graph.
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
LegendClust	Legends for the clusters
ClustCenters	Should the cluster centers be plotted
UseClusterColors	Should the cluster colors be used in the plot
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.
PlotBinaryMeans	Plot the mean of the presence points for each variable
MinIncidence	Minimum incidence to keep a variable
ShowBox	Should a box around the poitns be plotted?
ColorSupContVars	Colors for the supplementary continuous variables
ColorSupBinVars	Colors for the supplementary binary variables
ColorSupOrdVars	Colors for the supplementary ordinal variables
TypeScale	Type of scales for the plot
SupMode	Mode of the supplementary variables
PlotSupVars	Should the supplementary variables be plotted
...	Additional parameters for graphical representations

Details

Graphical representation of an Principal coordinates Analysis controlling visual aspects of the plot as colors, symbols or sizes of the points.

Value

No value is returned

Author(s)

Jose Luis Vicente-Villardon

References

J.R. Demey, J.L. Vicente-Villardon, M.P. Galindo, A.Y. Zambrano, Identifying molecular markers associated with classifications of genotypes by external logistic biplot, Bioinformatics 24 (2008) 2832.

See Also

BinaryProximities

Examples

data(spiders)
dist=BinaryProximities(spiders)
pco=PrincipalCoordinates(dist)
plot(pco)

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