plot.PERMANOVA: Plots the results of the PERMANOVA function

In PERMANOVA: Multivariate Analysis of Variance Based on Distances and Permutations

Description

Plots the principal coordinates of the group centers a the bootstrap confidence regions.

Usage

## S3 method for class 'PERMANOVA'
plot(x, A1 = 1, A2 = 2, ScaleGraph = TRUE, ShowAxis = FALSE,
ShowAxes = FALSE, LabelAxes = TRUE, margin = 0.1, ShowBox = TRUE, PlotGroups = TRUE,
LabelGroups = TRUE, CexGroup = 1.5, PchGroup = 16, ColorGroup = NULL, voronoi = TRUE,
VoronoiColor = "black", PlotInd = FALSE, 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 "PERMANOVA"
A1	Dimension for the first axis. 1 is the default.
A2	Dimension for the second axis. 2 is the default.
ScaleGraph	Resale the coordinates to optimal matching.
ShowAxis	Should the axis passing trough the origin be plotted?
ShowAxes	Should the axes be shown?
LabelAxes	Should the axes be labelled?
margin	Margin for labels (in percentage).
ShowBox	Should a box around the points be plotted?
PlotGroups	Should the group centers be plotted?
LabelGroups	Should the groups be labelled?
CexGroup	Size of the points for groups.
PchGroup	Mark of the points for groups.
ColorGroup	User colors for the groups. Default colors will be used if NULL.
voronoi	Should the Voronoi diagram with the prediction regions for each group be plotted?
VoronoiColor	Color for the Voronoi diagram.
PlotInd	Should the individuals be plotted?
LabelInd	Should the individuals be labelled?
CexInd	Size of the points for individuals.
PchInd	Markers of the points for individuals.
ColorInd	User colors for the individuals. Default colors will be used if NULL.
WhatInds	What individuals should be plotted? A vector.
IndLabels	Labels for the individuals.
PlotVars	Should the variables be plotted?
LabelVar	Should the variables be labelled?
CexVar	Size of the points for variables.
PchVar	Markers of the points for variables.
ColorVar	Colors of the points for variables.
WhatVars	What variables should be plotted? A vector.
VarLabels	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	Should the labels be plotted 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). By default is "M".
MinQualityVars	Minimum quality of representation for a variable to be plotted.
dpg	A set of indices with the variables that will show projections onto the variables.
dpi	A set of indices with the individuals that will show the projections.
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 parameter.

Details

Plots the principal coordinates of the group centers a the bootstrap confidence regions.

Value

The plot.

Author(s)

Laura Vicente-Gonzalez, Jose Luis Vicente-Villardon

Examples

data(wine)
X = wine[,4:21]
X=IniTransform(X)
D = DistContinuous (X)
perwine=PERMANOVA(D, wine$Group, CoordPrinc=TRUE)
plot(perwine)

PERMANOVA documentation built on Sept. 6, 2021, 5:07 p.m.