plot.MANOVA: Plots the results of a MANOVA Biplot

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

Description

Plots the results of a MANOVA Biplot.

Usage

## S3 method for class 'MANOVA'
plot(x, A1 = 1, A2 = 2, ScaleGraph = TRUE, PlotGroups = TRUE,
PlotVars = TRUE, PlotInd = TRUE, WhatInds=NULL,WhatVars=NULL, WhatGroups=NULL,
IndLabels=NULL, VarLabels=NULL, GroupLabels=NULL, AbbreviateLabels=FALSE,
LabelInd=TRUE, LabelVars = TRUE, CexGroup=1, PchGroup=16, margin=0.1,
AddLegend=FALSE, ShowAxes=FALSE, LabelAxes=FALSE, LabelGroups=TRUE,
PlotCircle = TRUE, ConvexHulls = FALSE, TypeCircle = "M", ColorGroups = NULL,
ColorVars = NULL, LegendPos="topright", ColorInd = NULL, voronoi = TRUE,
mode="a", TypeScale = "Complete", ValuesScale = "Original", MinQualityVars = 0,
dpg = 0, dpi=0, dp=0,  PredPoints=0, PlotAxis = FALSE, CexInd = NULL,
CexVar = NULL, PchInd = NULL, PchVar = NULL, ColorVar=NULL, ShowAxis=FALSE,
VoronoiColor="black", ShowBox=FALSE, ShowTitle=TRUE,PlotClus = FALSE,
TypeClus = "ch", ClustConf = 1, ClustCenters = FALSE, UseClusterColors = TRUE,
CexClustCenters=1, ...)

Arguments

x	An object of class "MANOVA.Biplot".
A1	Dimension for the first axis. 1 is the default.
A2	Dimension for the second axis. 2 is the default.
ScaleGraph	Rescale the coordinates to optimal matching.
PlotGroups	Should the group centers be plotted?
PlotVars	Should the variables be plotted?
PlotInd	Should the individuals be plotted?
WhatInds	What individuals should be plotted? A vector.
WhatVars	What variables should be plotted? A vector.
WhatGroups	What groups should be plotted? A vector.
IndLabels	Labels for the individuals.
VarLabels	Labels for the variables.
GroupLabels	Labels for the groups.
AbbreviateLabels	Should the labels be Abbreviated for simplicity of the graph?
LabelInd	Should the individuals be labelled?
LabelVars	Should the variables be labelled?
CexGroup	Size of the points for groups.
PchGroup	Mark of the points for groups.
margin	Margin for labels (in percentage).
AddLegend	Should a legend be added?
ShowAxes	Should the axes be shown?
LabelAxes	Should the axes be labelled?
LabelGroups	Should the groups be labelled?
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".
ColorGroups	User colors for the groups. Default colors will be used if NULL.
ColorVars	User colors for the variables. Default colors will be used if NULL.
LegendPos	Position of the legend.
ColorInd	User colors for the individuals. Default colors will be used if NULL.
voronoi	Should the Voronoi diagram with the prediction regions for each group be plotted?
mode	Mode of the biplot: "p", "a", "b", "h", "ah" and "s". See details.
TypeScale	Type of scale to use : "Complete", "StdDev" or "BoxPlot". See details.
ValuesScale	Values to show on the scale: "Original" or "Transformed".
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.
dp	A set of indices with the variables that will show the projections of the individuals.
PredPoints	A vector with integers. The group centers listed in the vector are projected onto all the variables.
PlotAxis	Not Used
CexInd	Size of the points for individuals.
CexVar	Size of the points for variables.
PchInd	Markers of the points for individuals.
PchVar	Markers of the points for variables.
ColorVar	Colors of the points for variables.
ShowAxis	Should axis scales be shown?
VoronoiColor	Color for the Voronoi diagram.
ShowBox	Should a box around the points be plotted?
ShowTitle	Should Title be shown?
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.
ClustCenters	Should the cluster centers be plotted?
UseClusterColors	Should the cluster colors be used in the plot?
CexClustCenters	Size of the cluster centres.
...	Any other graphical parameter.

Details

The function plots the results of a MANOVA Biplot. The coordinates for Groups, Individuals and Variables can be shown or not on the plot, each of the three can also be labeled separately. The are parameters to control the way each different set of coordinates is plotted and labeled.

There are several modes for plotting the biplot.

"p".- Points (Rows and Columns are represented by points)

"a" .- Arrows (The traditional representation with points for rows and arrows for columns)

"b" .- The arrows for the columns are extended to both extremes of the plot and labeled outside the plot area.

"h" .- The arrows for the columns are extended to the positive extreme of the plot and labeled outside the plot area.

"ah" .- Same as arrows but labeled outside the plot area.

"s" .- The directions (or biplot axes) have a graded scale for prediction of the original values.

The TypeScale argument applies only to the "s" mode. There are three types:

"Complete" .- An equally spaced scale covering the whole range of the data is calculates.

"StdDev" .- Mean with one, two and three standard deviations

"BoxPlot" .- Box-Plot like Scale (Median, 25 and 75 percentiles, maximum and minimum values.)

The ValuesScale argument applies only to the "s" mode and controls if the labels show the Original ot Transformed values.

Some of the initial transformations are not compatible with some of the types of biplots and scales. For example, It is not possible to recover by projection the original values when you double centre de data. In that case you have the residuals for interaction and only the transformed values make sense.

Value

A plot is returned.

Author(s)

Jose Luis Vicente-Villardon, Laura Vicente-Gonzalez

References

Gabriel, K. R. (1972). Analysis of meteorological data by means of canonical decomposition and biplots. Journal of Applied Meteorology, 11(7), 1071-1077.

Amaro, I. R., Vicente-Villardon, J. L., & Galindo Villardon, M. P. (2004). Manova Biplot para arreglos de tratamientos con dos factores basado en modelos lineales generales multivariantes. Interciencia, 29(1), 26-32.

Sierra, C., Ruiz-Barzola, O., Menendez, M., Demey, J. R., & Vicente-Villardon, J. L. (2017). Geochemical interactions study in surface river sediments at an artisanal mining area by means of Canonical (MANOVA)-Biplot. Journal of Geochemical Exploration, 175, 72-81.

Examples

data(wine)
X=wine[,4:21]
manbip=MANOVA(X, Group=wine$Group)
plot(manbip, TypeCircle="B", Voronoi=FALSE)

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