Plots the results of the PERMANOVA function
Plots the principal coordinates of the group centers a the bootstrap confidence regions.
## 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, PlotContrasts = FALSE, IndLimits=FALSE, ...)
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. |
PlotContrasts |
Should the contrasts be plotted? |
IndLimits |
Should the limits of the graph include all the individuals? |
... |
Any other graphical parameter. |
Plots the principal coordinates of the group centers a the bootstrap confidence regions.
The plot.
Laura Vicente-Gonzalez, Jose Luis Vicente-Villardon
data(wine) X = wine[,4:21] X=IniTransform(X) D = DistContinuous (X) perwine=PERMANOVA(D, wine$Group, CoordPrinc=TRUE) plot(perwine)
Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.