STATegRa (version 1.0.0)

plotRes: Plot results of Components Analysis

Description

Function that allows to plot scatterplots for scores or loadings, for common and distinctive part as well as combined plots for plotting both parts together. Different combinations of the parameters produce different plots.

Usage

plotRes(object, comps=c(1,2), what, type, combined, block, color=NULL, shape=NULL, labels=NULL, background=TRUE, palette=NULL, pointSize=4, labelSize=NULL, axisSize=NULL, titleSize=NULL)

Arguments

object

caClass object containing results of Components Analysis

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.

what

what=c("scores","loadings"). Are scores or loadings had to be represented?

type

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

combined

Logical indicating if the plot is a simple plot representing two components from the same block of information, or combined representing in the same plot two component each of them from a different block of information.

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)

color

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

shape

Character indicating with column of the pData in the initial ExpressionSet has to be used to set shape in the graph.

labels

Character indicating with column of the pData in the initial ExpressionSet has to be used to set labels in the graph.

background

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

palette

Vector indicating the pallete of colors used for the plot. See ggplot

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)

# Scatterplot of scores variables associated to common components

# DISCO-SCA
plotRes(object=discoRes,comps=c(1,2),what="scores",type="common",
        combined=FALSE,block="",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="",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="",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)

# Combined plot
plotRes(object=discoRes,comps=c(1,1),what="loadings",type="individual",
        combined=TRUE,block="",color="classname",shape=NULL,
        labels=NULL,background=TRUE,palette=NULL,pointSize=4,
        labelSize=NULL,axisSize=NULL,titleSize=NULL)