Plots the results of a Binary Logistic Biplot
# S3 method for 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, ...)The plot of the biplot.
An object of class Binary.Logistic.Biplot
Dimension for the first axis of the representation. Default = 1
Dimension for the second axis of the representation. Default = 2
Should the axis of the representation be shown?
Margin of the plot as a percentage. It gets some space for the labels.
Should the variables be plotted?
Should the individuals be plotted?
What Rows should be plotted. A binary vector containing which rows (individuals) should be plotted (1) and which should not (0).
What Columns should be plotted. A binary vector containing which columns (variables) should be plotted (1) and which should not (0).
Should the individuals be labeled?
Should the individuals be labeled?
Should a box around the points be plotted?
A vector of row labels. If NULL the labels contained in the object will be used.
A vector of column labels. If NULL the labels contained in the object will be used.
A vector of alternative row colors.
A vector of alternative column colors.
Mode of the biplot: "p", "a", "b", "h", "ah" and "s".
Length of the scale ticks for the biplot variables.
Cex (Size) of the rows (marks and labels). Can be a single common size for all the points or a vector with individual sizes.
Cex (Size) of the columns (marks and labels). Can be a single common size for all the points or a vector with individual sizes.
Should the labels be placed in a smart way?
Minimum quality of the rows to be plotted. (Between 0 and 1)
Minimum quality of the columns to be plotted. (Between 0 and 1)
A vector of variable indices to project all the individuals onto each variable of the vector.
A vector of row indices to project onto each variable.
Should the size of the Row points be related to its quality?
Should the size of the Column points be related to its quality?
Should the color of the Row points be related to its quality?
Should the color of the Column points be related to its quality?
Marks for the rows (numbers). Can be a single common mark for all the points or a vector with individual marks.
Marks for the columns (numbers). Can be a single common mark for all the points or a vector with individual marks.
Should the clusters be plotted?
Type of plot for the clusters. ("ch"- Convex Hull, "el"- Ellipse or "st"- Star)
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
Should only the significant variables be plotted?
Signification level.
Should the Bonferroni correction be used?
Should the Supplementary variables be plotted?
Should labels be abbreviated?
Should the mail Title be displayed?
Title to display.
Should the axis labs be removed?
Size of the point for 0.5 probability.
Any other graphical parameter.
Jose Luis Vicente Villardon
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.
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.
data(spiders)
X=Dataframe2BinaryMatrix(spiders)
logbip=BinaryLogBiplotGD(X,penalization=0.1)
plot(logbip, Mode="a")
summary(logbip)
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