STATegRa (version 1.0.0)

biplotRes: Biplot results of Components Analysis

Description

Function to display a biplot of an caClass object coming from a Component Analysis.

Usage

biplotRes(object,type,comps,block,title=NULL,colorCol=NULL,sizeValues=c(2,4), shapeValues=c(17,0),background=TRUE,pointSize=4,labelSize=NULL, axisSize=NULL,titleSize=NULL)

Arguments

object

caClass object containing results of Components Analysis

type

Indicate which components should be represented, "common", "individual" or "both" in the case of combined plots

comps

Components to plot. If combined=FALSE, it indicates the x and y components of the type and block chosen. If combined=TRUE, it indicates the component to plot for the first block of information and the component for the second block of information to plot together. By default the components are set to c(1,2) if combined=FALSE and to c(1,1) if combined=TRUE.

block

Indicates which block has to be represented. It can be specify by a numeric value (1 or 2) or a character (name of the block in the input data provided to the omicCompAnalysis() analysis)

title

Title of the biplot

colorCol

Character indicating with column of the pData in the initial ExpressionSet has to be used to set color in the graph. By default is the first column of the pData

sizeValues

Vector indicating which sizes has to be use for scores and loadings?

shapeValues

Vector indicating which shapes has to be used for scores and loadings

background

Logical indicating if the plot have to be represented with grey background or not

pointSize

Size of the points represented in the plot

labelSize

Size of the labels if label is not NULL

axisSize

Size of the text in the axis of the plot

titleSize

Size of main title

Value

Plot of class ggplot

See Also

ggplot,omicsCompAnalysis

Examples

data("STATegRa_S3")
B1 <- createOmicsExpressionSet(Data=Block1.PCA,pData=ed.PCA,
                               pDataDescr=c("classname"))
B2 <- createOmicsExpressionSet(Data=Block2.PCA,
                               pData=ed.PCA,pDataDescr=c("classname"))
# Omics components analysis
discoRes <- omicsCompAnalysis(Input=list(B1,B2),Names=c("expr","mirna"),
                              method="DISCOSCA",Rcommon=2,Rspecific=c(2,2),
                              center=TRUE,scale=TRUE,weight=TRUE)
jiveRes <- omicsCompAnalysis(Input=list(B1,B2),Names=c("expr","mirna"),
                              method="JIVE",Rcommon=2,Rspecific=c(2,2),
                              center=TRUE,scale=TRUE,weight=TRUE)

o2plsRes <- omicsCompAnalysis(Input=list(B1,B2),Names=c("expr","mirna"),
                              method="O2PLS",Rcommon=2,Rspecific=c(2,2),
                              center=TRUE,scale=TRUE,weight=TRUE)

# Biplot common part. DISCO-SCA

biplotRes(object=discoRes,type="common",comps=c(1,2),block="",
          title=NULL,colorCol="classname",sizeValues=c(2,4),
          shapeValues=c(17,0),background=TRUE,pointSize=4,
          labelSize=NULL,axisSize=NULL,titleSize=NULL)

# Biplot common part. O2PLS

p1 <- biplotRes(object=o2plsRes,type="common",comps=c(1,2),
          block="expr",title=NULL,colorCol="classname",
          sizeValues=c(2,4),shapeValues=c(17,0),
          background=TRUE,pointSize=4,labelSize=NULL,
          axisSize=NULL,titleSize=NULL)
p2 <- biplotRes(object=o2plsRes,type="common",comps=c(1,2),
          block="mirna",title=NULL,colorCol="classname",
          sizeValues=c(2,4),shapeValues=c(17,0),
          background=TRUE,pointSize=4,labelSize=NULL,
          axisSize=NULL,titleSize=NULL)

# Biplot distinctive part. O2PLS

p1 <- biplotRes(object=discoRes,type="individual",comps=c(1,2),
          block="expr",title=NULL,colorCol="classname",
          sizeValues=c(2,4),shapeValues=c(17,0),
          background=TRUE,pointSize=4,labelSize=NULL,
          axisSize=NULL,titleSize=NULL)
p2 <- biplotRes(object=discoRes,type="individual",comps=c(1,2),
          block="mirna",title=NULL,colorCol="classname",
          sizeValues=c(2,4),shapeValues=c(17,0),
          background=TRUE,pointSize=4,labelSize=NULL,
          axisSize=NULL,titleSize=NULL)