plotRes: Plot component analysis results

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

Description

Plot scatterplots of scores or loadings, for common and distinctive parts as well as combined plots.

Usage

plotRes(object, comps=c(1, 2), what, type, combined, block=NULL, 
               color=NULL, shape=NULL, labels=NULL, title=NULL, xlabel=NULL, ylabel=NULL, background=TRUE, 
               palette=NULL, pointSize=4, labelSize=NULL, 
               axisSize=NULL, titleSize=NULL, sizeValues = c(2,4), shapeValues = c(17, 0))

Arguments

object	caClass-class containing component analysis results
comps	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.
what	Either "scores", "loadings" or "both"
type	Either "common", "individual" or "both"
combined	Logical indicating whether to make a simple plot of two components from one block, or components from different blocks
block	Which block to plot, either "1" or "2" or the name of the block.
color	Character specifying a pData column from the original data to use to color points
shape	Character specifying a pData column to select point shape
labels	Character specifying a pData column from which to take point labels
title	Main title
xlabel	x-axis name
ylabel	y-axis name
background	Logical specifying whether to make a grey background
palette	Vector giving the color palette for the plot
pointSize	Size of plot points
labelSize	Size of point labels if not NULL
axisSize	Size of axis text
titleSize	Size of title text
sizeValues	Vector containing sizes for scores and loadings
shapeValues	Vector indicating the shapes for scores and loadings

Value

ggplot 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)

# Scatterplot of scores variables associated to common components

# DISCO-SCA
plotRes(object=discoRes,comps=c(1,2),what="scores",type="common",
        combined=FALSE,block=NULL,color="classname",shape=NULL,labels=NULL,
        background=TRUE,palette=NULL,pointSize=4,labelSize=NULL,
        axisSize=NULL,titleSize=NULL)
# JIVE
plotRes(object=jiveRes,comps=c(1,2),what="scores",type="common",
       combined=FALSE,block=NULL,color="classname",shape=NULL,labels=NULL,
        background=TRUE,palette=NULL,pointSize=4,labelSize=NULL,
        axisSize=NULL,titleSize=NULL)

# O2PLS
# Scatterplot of scores variables associated to common components
# Associated to first block
p1 <- plotRes(object=o2plsRes,comps=c(1,2),what="scores",type="common",
              combined=FALSE,block="expr",color="classname",shape=NULL,
              labels=NULL,background=TRUE,palette=NULL,pointSize=4,
              labelSize=NULL,axisSize=NULL,titleSize=NULL)
# Associated to second block
p2 <- plotRes(object=o2plsRes,comps=c(1,2),what="scores",type="common",
              combined=FALSE,block="mirna",color="classname",shape=NULL,
              labels=NULL,background=TRUE,palette=NULL,pointSize=4,
              labelSize=NULL,axisSize=NULL,titleSize=NULL)

# Combined plot of scores variables assocaited to common components
plotRes(object=o2plsRes,comps=c(1,1),what="scores",type="common",
        combined=TRUE,block=NULL,color="classname",shape=NULL,
        labels=NULL,background=TRUE,palette=NULL,pointSize=4,
        labelSize=NULL,axisSize=NULL,titleSize=NULL)

# Loadings plot for individual components
# Separately for each block
p1 <- plotRes(object=discoRes,comps=c(1,2),what="loadings",type="individual",
              combined=FALSE,block="expr",color="classname",shape=NULL,
              labels=NULL,background=TRUE,palette=NULL,pointSize=4,
              labelSize=NULL,axisSize=NULL,titleSize=NULL)
p2 <- plotRes(object=discoRes,comps=c(1,2),what="loadings",type="individual",
              combined=FALSE,block="mirna",color="classname",shape=NULL,
              labels=NULL,background=TRUE,palette=NULL,pointSize=4,
              labelSize=NULL,axisSize=NULL,titleSize=NULL)

# Biplot: scores + loadings
plotRes(object=discoRes,comps=c(1,2),what="both",type="common",
        combined=FALSE,block="expr",color="classname",shape=NULL,
        labels=NULL,background=TRUE,palette=NULL,pointSize=4,
        labelSize=NULL,axisSize=NULL,titleSize=NULL)

STATegRa documentation built on Nov. 8, 2020, 5:26 p.m.