plot.Binary.Logistic.Biplot: Plots the results of a Binary Logistic Biplot

In MultBiplotR: Multivariate Analysis Using Biplots in R

Plots the results of a Binary Logistic Biplot

Description

Plots the results of a Binary Logistic Biplot

Usage

## S3 method for class 'Binary.Logistic.Biplot'
plot(x, F1 = 1, F2 = 2, ShowAxis = FALSE, margin = 0, 
PlotVars = TRUE, PlotInd = TRUE, WhatRows = NULL, WhatCols = NULL, 
LabelRows = TRUE, LabelCols = TRUE, ShowBox = FALSE, RowLabels = NULL, 
ColLabels = NULL, RowColors = NULL, ColColors = NULL, Mode = "s", 
TickLength = 0.01, RowCex = 0.8, ColCex = 0.8, SmartLabels = FALSE, 
MinQualityRows = 0, MinQualityCols = 0, dp = 0, PredPoints = 0, 
SizeQualRows = FALSE, SizeQualCols = FALSE, ColorQualRows = FALSE, 
ColorQualCols = FALSE, PchRows = NULL, PchCols = NULL, PlotClus = FALSE, 
TypeClus = "ch", ClustConf = 1, Significant = TRUE, alpha = 0.05, 
Bonferroni = TRUE, PlotSupVars = TRUE, AbbreviateLabels = FALSE, MainTitle = TRUE, Title =
                    NULL, RemoveXYlabs = FALSE, CenterCex = 1.5,  ...)

Arguments

x	An object of class Binary.Logistic.Biplot
F1	Dimension for the first axis of the representation. Default = 1
F2	Dimension for the second axis of the representation. Default = 2
ShowAxis	Should the axis of the representation be shown?
margin	Margin of the plot as a percentage. It gets some space for the labels.
PlotVars	Should the variables be plotted?
PlotInd	Should the individuals be plotted?
WhatRows	What Rows should be plotted. A binary vector containing which rows (individuals) should be plotted (1) and which should not (0).
WhatCols	What Columns should be plotted. A binary vector containing which columns (variables) should be plotted (1) and which should not (0).
LabelRows	Should the individuals be labeled?
LabelCols	Should the individuals be labeled?
ShowBox	Should a box around the points be plotted?
RowLabels	A vector of row labels. If NULL the labels contained in the object will be used.
ColLabels	A vector of column labels. If NULL the labels contained in the object will be used.
RowColors	A vector of alternative row colors.
ColColors	A vector of alternative column colors.
Mode	Mode of the biplot: "p", "a", "b", "h", "ah" and "s".
TickLength	Length of the scale ticks for the biplot variables.
RowCex	Cex (Size) of the rows (marks and labels). Can be a single common size for all the points or a vector with individual sizes.
ColCex	Cex (Size) of the columns (marks and labels). Can be a single common size for all the points or a vector with individual sizes.
SmartLabels	Should the labels be placed in a smart way?
MinQualityRows	Minimum quality of the rows to be plotted. (Between 0 and 1)
MinQualityCols	Minimum quality of the columns to be plotted. (Between 0 and 1)
dp	A vector of variable indices to project all the individuals onto each variable of the vector.
PredPoints	A vector of row indices to project onto each variable.
SizeQualRows	Should the size of the Row points be related to its quality?
SizeQualCols	Should the size of the Column points be related to its quality?
ColorQualRows	Should the color of the Row points be related to its quality?
ColorQualCols	Should the color of the Column points be related to its quality?
PchRows	Marks for the rows (numbers). Can be a single common mark for all the points or a vector with individual marks.
PchCols	Marks for the columns (numbers). Can be a single common mark for all the points or a vector with individual marks.
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
Significant	Should only the significant variables be plotted?
alpha	Signification level.
Bonferroni	Should the Bonferroni correction be used?
PlotSupVars	Should the Supplementary variables be plotted?
AbbreviateLabels	Should labels be abbreviated?
MainTitle	Should the mail Title be displayed?
Title	Title to display.
RemoveXYlabs	Should the axis labs be removed?
CenterCex	Size of the point for 0.5 probability.
...	Any other graphical parameter.

Details

Plots a biplot for binary data. The Biplot for binary 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.

Value

The plot of the biplot.

Author(s)

Jose Luis Vicente Villardon

References

Vicente-Villardon, J. L., Galindo, M. P. and Blazquez, A. (2006) Logistic Biplots. In Multiple Correspondence Análisis And Related Methods. Grenacre, M & Blasius, J, Eds, Chapman and Hall, Boca Raton.

Demey, J., Vicente-Villardon, J. L., Galindo, M.P. AND Zambrano, A. (2008) Identifying Molecular Markers Associated With Classification Of Genotypes Using External Logistic Biplots. Bioinformatics, 24(24): 2832-2838.

Examples

data(spiders)
X=Dataframe2BinaryMatrix(spiders)

logbip=BinaryLogBiplotGD(X,penalization=0.1)
plot(logbip, Mode="a")
summary(logbip)

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