plotVAF {STATegRa} | R Documentation

## Plot VAF (Variance Explained For) from Component Analysis

### Description

This function visualises the VAF results from component analysis. The input is a `caClass-class` object from `omicsCompAnalysis`. VAF cannot be calculated if mode "O2PLS" was used. The plots for modes "DISCOSCA" and "JIVE" are different since DISCO-SCA distinctive components have some VAF in the other block. This VAF can be interpreted as an error in the rotation.

### Usage

    plotVAF(object, mainTitle="")

### Arguments

`object` | `caClass-class` object containing component analysis results
`mainTitle` | Plot title

### Value

`ggplot` object

### Author(s)

Patricia Sebastian-Leon

### Examples

    data("STATegRa_S3")
    require(ggplot2)
    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)

    # DISCO-SCA plotVAF
    plotVAF(discoRes)

    # JIVE plotVAF
    plotVAF(jiveRes)

[Package STATegRa version 1.16.1 Index]