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

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/plot.Principal.Coordinates.R

Description

Plots an object of class Principal.Coordinates

Usage

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## 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
PlotBinaryMeans
MinIncidence
ShowBox
ColorSupContVars
ColorSupBinVars
ColorSupOrdVars
TypeScale
SupMode
PlotSupVars
...

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

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villardon/MultBiplotR documentation built on June 5, 2021, 8:55 a.m.