SelectVar-Biplot: Plot a 'Biplot' of a SelectVar class object

In kimod: A k-tables approach to integrate multiple Omics-Data

Description

Plot a Biplot of a SelectVar class object

Usage

## S4 method for signature 'SelectVar'
Biplot(x,xlab=NULL, ylab=NULL, mainP=NULL,
xlimi=NULL, ylimi=NULL, labelObs=TRUE,labelVars= TRUE,
colVar= "black",colObs="black",
 pchPoints=15,Type=c("RMP","CMP","SQRT","HJ"),
 Groups=FALSE,NGroups=2 ,...)

Arguments

x	DiStatis class object.
xlab	character for the x-label title for plot
ylab	character for the x-label title for plot
mainP	the main Biplot
xlimi	(vector) Bounds to x-axis
ylimi	(vector) Bounds to y-axis
labelObs	Logical. indicates whether the labels of observations are prints. Default is TRUE
labelVars	Logical. indicates whether the labels of variables are prints. Default is TRUE
colVar	character col for colours of the variables in the plot. Default is black.
colObs	character col for colours of the observations in the plot. Default is black.
pchPoints	Either an integer specifying a symbol or a single character to be used as the default in plotting points.
Type	type of Biplot. Options are CMP RMP SQRT or HJ.
Groups	Logical. If is TRUE, the variables are grouped. See GroupProj
NGroups	Only if the Groups are TRUE. Indicate the number the groups of variables.
...	additional parameters for plot

Value

plotted Biplot/s of the component/s of the given SelectVar object.

Author(s)

M L Zingaretti, J A Demey-Zambrano, J L Vicente Villardon, J R Demey

Examples

{
data(NCI60Selec)
Z1<-DiStatis(NCI60Selec)
M1<-SelectVar(Z1,Crit="R2-Adj")
Colores1<-c(rep("Breast",5),rep("CNS",6),rep("Colon",7),
rep("Leukemia",6),rep("Melanoma",10),rep("Lung",9),
rep("Ovarian",7),rep("Prostate",2),rep("Renal",8))
Colores2<-c(rep(colors()[657],5),rep(colors()[637],6),
rep(colors()[537],7),rep(colors()[552],6),rep(colors()[57],10)
,rep(colors()[300],9),rep(colors()[461],7),rep(colors()[450],2)
,rep(colors()[432],8))
Biplot(M1,labelObs = FALSE,labelVars=FALSE,
colObs=Colores2,Type="SQRT",las=1,cex.axis=0.8,
cex.lab=0.8,xlimi=c(-3,3),ylimi=c(-3,3))
legend("topright",unique(Colores1),col=unique(Colores2),
bty="n",pch=16,cex=0.6)
Biplot(M1,labelObs = FALSE,labelVars=TRUE,colObs=Colores2,
Type="SQRT",las=1,cex.axis=0.8,cex.lab=0.8,xlimi=c(-3,3),
ylimi=c(-3,3),Groups=TRUE,NGroups=6)
legend("topright",unique(Colores1),col=unique(Colores2),
bty="n",pch=16,cex=0.6)
data(winesassesors)
Z3<-DiStatis(winesassesors)
M3<-SelectVar(Z3,Crit="R2-Adj")
Col1<-c(rep("NZ",4),rep("FR",4),rep("CA",4))
Col2<-c(rep(2,4),rep(3,4),rep(4,4))
Biplot(M3,labelObs=FALSE,labelVars=TRUE,colObs=Col2,
Type="SQRT",xlimi=c(-2,2),ylimi=c(-2,2),las=1,cex.axis=0.8,
cex.lab=0.8)
legend("topright",unique(Col1),col=unique(Col2),bty="n",pch=16,cex=0.8)
Biplot(M1,labelObs = FALSE,labelVars=FALSE,colObs=Colores2,
Type="CMP")
legend("topright",unique(Colores1),
col=unique(Colores2),bty="n",pch=16,cex=1)

}

Example output

The calculations were performed using the scalar product between the tables
The Projection of all variables will be made when the number of variables is less than 50
The calculations were performed using the scalar product between the tables
The Projection of all variables will be made when the number of variables is less than 50

kimod documentation built on April 28, 2020, 9:21 p.m.