plot.ContinuousBiplot: Plots a biplot for continuous data.

In MultBiplotR: Multivariate Analysis Using Biplots in R

Plots a biplot for continuous data.

Description

Plots a biplot for continuous data.

Usage

## S3 method for class 'ContinuousBiplot'
plot(x, A1 = 1, A2 = 2, ShowAxis = FALSE, margin = 0,
                    PlotVars = TRUE, PlotInd = TRUE, WhatInds = NULL,
                    WhatVars = NULL, LabelVars = TRUE, LabelInd = TRUE,
                    IndLabels = NULL, VarLabels = NULL, mode = "a", CexInd
                    = NULL, CexVar = NULL, ColorInd = NULL, ColorVar =
                    NULL, LabelPos = 1, SmartLabels = FALSE,
                    AbbreviateLabels = FALSE, MinQualityInds = 0,
                    MinQualityVars = 0, dp = 0, PredPoints = 0, PlotAxis =
                    FALSE, TypeScale = "Complete", ValuesScale =
                    "Original", SizeQualInd = FALSE, SizeQualVars = FALSE,
                    ColorQualInd = FALSE, ColorQualVars = FALSE, PchInd =
                    NULL, PchVar = NULL, PlotClus = FALSE, TypeClus =
                    "ch", ClustConf = 1, ClustLegend = FALSE,
                    ClustLegendPos = "topright", ClustCenters = FALSE,
                    UseClusterColors = TRUE, CexClustCenters = 1,
                    PlotSupVars = TRUE, SupMode = "a", ShowBox = FALSE,
                    nticks = 5, NonSelectedGray = FALSE, PlotUnitCircle =
                    TRUE, PlotContribFA = TRUE, AddArrow = FALSE,
                    ColorSupContVars = "red", ColorSupBinVars = "red",
                    ColorSupOrdVars = "red", ModeSupContVars="a", 
                    ModeSupBinVars="a", ModeSupOrdVars="a", 
                    WhatSupBinVars = NULL, Title = NULL, Xlab = NULL, 
                    Ylab = NULL, add = FALSE, PlotTrajVars = FALSE, 
                    PlotTrajInds = FALSE, LabelTraj = "end", Limits = NULL,
                    PlotSupInds = FALSE, WhatSupInds = NULL,
                    ColorSupInd = "black", CexSupInd = 0.8, PchSupInd =
                   16, LabelSupInd = TRUE, PredSupPoints = 0,  CexScale =
                    0.5, ...)

Arguments

x	An object of class "Biplot"
A1	Dimension for the first axis. 1 is the default.
A2	Dimension for the second axis. 2 is the default.
ShowAxis	Logical variable to control if the coordinate axes should appear in the plot. The default value is FALSE because for most of the biplots its presence is irrelevant.
margin	Margin for the labels in some of the biplot modes (percentage of the plot width). Default is 0. Increase the value if the labels are not completely plotted.
PlotVars	Logical to control if the Variables (Columns) are plotted.
PlotInd	Logical to control if the Individuals (Rows) are 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)
LabelVars	Logical to control if the labels for the Variables are shown
LabelInd	Logical to control if the labels for the individuals are shown
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
mode	Mode of the biplot: "p", "a", "b", "h", "ah" and "s".
CexInd	Size for the symbols and labels of the individuals. Can be a single common size for all the points or a vector with individual sizes.
CexVar	Size for the symbols and labels of the variables. Can be a single common size for all the points or a vector with individual sizes.
ColorInd	Color for the symbols and labels of the individuals. Can be a single common color for all the points or a vector with individual colors.
ColorVar	Color for the symbols and labels of the variables. Can be a single common color for all the points or a vector with individual colors.
LabelPos	Position of the labels in relation to the point. (Se the graphical parameter pos )
SmartLabels	Plot the labels in a smart way
AbbreviateLabels	Should labels be abbreviated?
MinQualityInds	Minimum quality of representation for an individual to be plotted.
MinQualityVars	Minimum quality of representation for a variable to be plotted.
dp	A set of indices with the variables that will show the projections of the individuals.
PredPoints	A vector with integers. The row points listed in the vector are projected onto all the variables.
PlotAxis	Not Used
TypeScale	Type of scale to use : "Complete", "StdDev" or "BoxPlot"
ValuesScale	Values to show on the scale: "Original" or "Transformed"
SizeQualInd	Should the size of the row points be related to their qualities of representation (predictiveness)?
SizeQualVars	Should the size of the column points be related to their qualities of representation (predictiveness)?
ColorQualInd	Should the color of the row points be related to their qualities of representation (predictiveness)?
ColorQualVars	Should the color of the column points be related to their qualities of representation (predictiveness)?
PchInd	Symbol for the row points. See help(points) for details.
PchVar	Symbol for the column points. See help(points) for details.
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
ClustLegend	Should a legend for the clusters be plotted? Default FALSE
ClustLegendPos	Position of the legend for the clusters. Default "topright"
ClustCenters	Should the cluster centers be plotted
UseClusterColors	Should the cluster colors be used in the plot
CexClustCenters	Size of the cluster centres
PlotSupVars	Should the supplementary variables be plotted?
SupMode	Mode of the supplementary variables.
ShowBox	Should a box around the poitns be plotted?
nticks	Number of ticks for the representation of the variables
NonSelectedGray	The nonselected individuals and variables aplotted in light gray colors
PlotUnitCircle	Plot the unit circle in the biplot for a Factor Analysis in which the lenght of the column arrows is smaller than 1 and is the quality of representation.
PlotContribFA	Plot circles in the biplot for a Factor Analysis with different values of the quality of representation.
AddArrow	Add an arrow to the representation of other modes of the biplot.
ColorSupContVars	Colors for the continuous supplementary variables.
ColorSupBinVars	Colors for the binary supplementary variables.
ColorSupOrdVars	Colors for the ordinal supplementary variables.
ModeSupContVars	Mode for the continuous supplementary variables.
ModeSupBinVars	Mode for the binary supplementary variables.
ModeSupOrdVars	Mode for the ordinal supplementary variables.
WhatSupBinVars	What supplementary binary variables should be plotted?
Title	Title of the plot.
Xlab	Label for the X axis
Ylab	Label for the Y axis
add	Should the plot be added to an existing plot?
PlotTrajVars	Plot trajectories for the variables (when appropriate)?
PlotTrajInds	Plot trajectories for the individuals (when appropriate)?
LabelTraj	Label trajectories for the variables (when appropriate)?
Limits	Limits of the axis for the plot
PlotSupInds	Should the supplementary individuals be plotted?
WhatSupInds	What supplementary individuals are going to be plotted
ColorSupInd	Colors for the supplementary individuals
CexSupInd	Sizes for the supplementary individuals
PchSupInd	Symbols for the supplementary individuals
LabelSupInd	Labels for the supplementary individuals
PredSupPoints	Predictions for the supplementary individuals
CexScale	Sizes of the scales
...	Any other graphical parameters.

Details

Plots a biplot for continuous data. The Biplot for continuous data is taken as the basis of the plot. If there are a mixture of different types of variables (binary, nominal, abundance, ...) are added to the biplot as supplementary parts.

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.

It is possible to associate the color and the size of the points with the quality of representation. Bigger points correspond to better representation quality.

Value

No value Returned

Author(s)

Jose Luis Vicente Villardon

References

Gabriel, K. R. (1971). The biplot graphic display of matrices with application to principal component analysis. Biometrika, 58(3), 453-467.

Galindo Villardon, M. (1986). Una alternativa de representacion simultanea: HJ-Biplot. Questiio. 1986, vol. 10, num. 1.

Vicente-Villardon, J. L., Galindo Villardon, M. P., & Blazquez Zaballos, A. (2006). Logistic biplots. Multiple correspondence analysis and related methods. London: Chapman & Hall, 503-521.

Gower, J. C., & Hand, D. J. (1995). Biplots (Vol. 54). CRC Press.

Gower, J. C., Lubbe, S. G., & Le Roux, N. J. (2011). Understanding biplots. John Wiley & Sons.

Blasius, J., Eilers, P. H., & Gower, J. (2009). Better biplots. Computational Statistics & Data Analysis, 53(8), 3145-3158.

Examples

data(Protein)
bip=PCA.Biplot(Protein[,3:11])
plot(bip, mode="s", margin=0.2, ShowAxis=FALSE)

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