plot.Canonical.Biplot: Plots a Canonical Biplot

In MultBiplotR: Multivariate Analysis Using Biplots in R

Plots a Canonical Biplot

Description

Plots a Canonical Biplot

Usage

## S3 method for class 'Canonical.Biplot'
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 "Canonical.Biplot"
A1	Dimension for the first axis. 1 is the default.
A2	Dimension for the second axis. 2 is the default.
ScaleGraph	Reescale the coordinates to optimal matching.
PlotGroups	Shoud the group centers be plotted?
PlotVars	Should the variables be plotted?
PlotInd	Should the individuals be plotted?
WhatInds	Logical vector to control what individuals (Rows) are plotted. (Can be also a binary vector)
WhatVars	Logical vector to control what variables (Columns) are plotted. (Can be also a binary vector)
WhatGroups	Logical vector to control what groups are plotted. (Can be also a binary vector)
IndLabels	A set of labels for the individuals. If NULL the default object labels are used
VarLabels	A set of labels for the variables. If NULL the default object labels are used
GroupLabels	A set of labels for the groups. If NULL the default object labels are used
AbbreviateLabels	Should labels be abbreviated?
LabelInd	Should the individuals be labeled?
LabelVars	Should the variables be labeled?
CexGroup	Sizes of the points for the groups
PchGroup	Markers for the group
margin	margin for the graph
AddLegend	Should a legend with the groups be added?
ShowAxes	Should outside axes be shown?
LabelAxes	Should outside axes be labelled?
LabelGroups	Should the groups be labeled?
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)
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 regións for each group be plotted?
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"
MinQualityVars	Minimum quality of representation for a variable to be plotted
dpg	A set of indices with the variables that will show the projections of the gorups
dpi	A set of indices with the individuasl that will show the projections on the variables
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	Marhers 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 poitns be plotted?
ShowTitle	Should the 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 parameters

Details

The function plots the results of a Canononical 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 stadard 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

No value returned

Author(s)

Jose Luis Vicente Villardon

References

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.

Varas, M. J., Vicente-Tavera, S., Molina, E., & Vicente-Villardon, J. L. (2005). Role of canonical biplot method in the study of building stones: an example from Spanish monumental heritage. Environmetrics, 16(4), 405-419.

Santana, M. A., Romay, G., Matehus, J., Villardon, J. L., & Demey, J. R. (2009). simple and low-cost strategy for micropropagation of cassava (Manihot esculenta Crantz). African Journal of Biotechnology, 8(16).

Examples

data(wine)
X=wine[,4:21]
canbip=CanonicalBiplot(X, group=wine$Group)
plot(canbip, TypeCircle="U")

MultBiplotR documentation built on Nov. 21, 2023, 5:08 p.m.