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

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(STATegRa)
Warning message:
replacing previous import 'Biobase::combine' by 'gridExtra::combine' when loading 'STATegRa' 
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/STATegRa/plotVAF.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotVAF
> ### Title: Plot VAF (Variance Explained For) from Component Analysis
> ### Aliases: plotVAF plotVAF,caClass-method
> 
> ### ** Examples
> 
> data("STATegRa_S3")
> require(ggplot2)
Loading required package: 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)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>