Plots the principal coordinates of the group centers a the bootstrap confidence regions.
# S3 method for 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, ...)An object of class "PERMANOVA"
Dimension for the first axis. 1 is the default.
Dimension for the second axis. 2 is the default.
Resale the coordinates to optimal matching.
Should the axis passing trough the origin be plotted?
Should the axes be shown?
Should the axes be labelled?
Margin for labels (in percentage).
Should a box around the points be plotted?
Should the group centers be plotted?
Should the groups be labelled?
Size of the points for groups.
Mark of the points for groups.
User colors for the groups. Default colors will be used if NULL.
Should the Voronoi diagram with the prediction regions for each group be plotted?
Color for the Voronoi diagram.
Should the individuals be plotted?
Should the individuals be labelled?
Size of the points for individuals.
Markers of the points for individuals.
User colors for the individuals. Default colors will be used if NULL.
What individuals should be plotted? A vector.
Labels for the individuals.
Should the variables be plotted?
Should the variables be labelled?
Size of the points for variables.
Markers of the points for variables.
Colors of the points for variables.
What variables should be plotted? A vector.
Labels for the variables.
Mode of the biplot: "p", "a", "b", "h", "ah" and "s".
Type of scale to use : "Complete", "StdDev" or "BoxPlot".
Values to show on the scale: "Original" or "Transformed".
Should the labels be plotted in a smart way?
Should a legend be added?
Position of the legend.
Should the confidence regions for the groups be plotted?
Should the convex hulls containing the individuals for each group be plotted?
Type of confidence region: Univariate (U), Bonferroni(B), Multivariate (M) or Classical (C). By default is "M".
Minimum quality of representation for a variable to be plotted.
A set of indices with the variables that will show projections onto the variables.
A set of indices with the individuals that will show the projections.
A vector with integers. The group centers listed in the vector are projected onto all the variables.
Should the clusters be plotted?
Type of plot for the clusters. ("ch"- Convex Hull, "el"- Ellipse or "st"- Star)
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.
Size of the cluster centers.
Should the cluster centers be plotted.
Should the cluster colors be used in the plot.
Any other graphical parameter.
The plot.
Plots the principal coordinates of the group centers a the bootstrap confidence regions.
# NOT RUN {
data(wine)
X = wine[,4:21]
X=IniTransform(X)
D = DistContinuous (X)
perwine=PERMANOVA(D, wine$Group, CoordPrinc=TRUE)
plot(perwine)
# }
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