biplotRes: Biplot of component analysis

In llrs/STATegRa: Classes and methods for multi-omics data integration

Description

Generate a biplot of component analysis results

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 component analysis results
type	Character specifying which components to plot; "common", "individual" or "both"
comps	Components to plot. If combined=FALSE, specifies the component indices to use as x and y for the plot. Otherwise, the component from the first block and the component from second block to plot together.
block	Which block to plot, either "1" or "2" or the name of the block.
title	Plot title
colorCol	Character specifying a pData column to use to colorise the plot points
sizeValues	Vector containing sizes for scores and loadings
shapeValues	Vector indicating the shapes for scores and loadings
background	Logical, whether to use a grey background
pointSize	Size of plot points
labelSize	Size of plot labels if not NULL
axisSize	Size of axis text
titleSize	Size of title text

Value

ggplot2 object

Author(s)

Patricia Sebastian-Leon

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)

llrs/STATegRa documentation built on May 29, 2019, 3:42 a.m.