plot.Principal.Coordinates function

Plots an object of class Principal.Coordinates

## 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.

Returns

No value is returned

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.

Author(s)

Jose Luis Vicente-Villardon

See Also

BinaryProximities

Examples

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