plotRes {STATegRa} | R Documentation |
Plot scatterplots of scores or loadings, for common and distinctive parts as well as combined plots.
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))
object |
|
comps |
If combined=FALSE, it indicates the x and y components of the type and block chosen. If |
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 |
ggplot
object
Patricia Sebastian-Leon
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)