## ----style, echo = FALSE, results = 'asis'------------------------------------ BiocStyle::markdown(css.files = c('custom.css')) ## ----------------------------------------------------------------------------- library(ade4) library(made4) library(scatterplot3d) ## ----eval=FALSE--------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("made4") ## ----------------------------------------------------------------------------- library(made4) library(ade4) data(khan) ## ----------------------------------------------------------------------------- names(khan) k.data<-khan$train k.class<-khan$train.classes ## ----overview.extra, eval=FALSE----------------------------------------------- # overview(k.data) ## ----overviewKhan,fig.width=7,fig.height=6, fig.cap="\\label{fig:fig1}Overview of Khan data."---- overview(k.data, labels=k.class) ## ----overviewKhan2,fig.width=7,fig.height=6, fig.cap="\\label{fig:fig2}Overview of Khan data."---- overview(k.data, classvec=k.class, labels=k.class) ## ----------------------------------------------------------------------------- k.coa<- ord(k.data, type="coa") ## ----output.coa--------------------------------------------------------------- names(k.coa) summary(k.coa$ord) ## ----see.classes-------------------------------------------------------------- k.class ## ----plotcoa------------------------------------------------------------------ plot(k.coa, classvec=k.class, genecol="grey3") ## ----plotgenesCOA,eval=FALSE-------------------------------------------------- # plotgenes(k.coa) ## ----plotarrays--------------------------------------------------------------- plotarrays(k.coa, arraylabels=k.class) ## ----plotarays2--------------------------------------------------------------- k.coa2<-ord(k.data, classvec=k.class) plot(k.coa2) ## ----plotgenes---------------------------------------------------------------- plotgenes(k.coa, n=5, col="red") ## ----plotgenescmd------------------------------------------------------------- gene.symbs<- khan$annotation$Symbol gene.symbs[1:4] ## ----plotgenesSym------------------------------------------------------------- plotgenes(k.coa, n=10, col="red", genelabels=gene.symbs) ## ----topgenes, eval=FALSE----------------------------------------------------- # topgenes(k.coa, axis = 1, n=5) ## ----topgenes2---------------------------------------------------------------- topgenes(k.coa, labels=gene.symbs, end="neg") ## ----do3d--------------------------------------------------------------------- do3d(k.coa$ord$co, classvec=k.class, cex.symbols=3) ## ----eval=FALSE--------------------------------------------------------------- # html3D(k.coa$ord$co, k.class, writehtml=TRUE) ## ----html3D, echo=FALSE, fig.cap="Output from html3D"------------------------- knitr::include_graphics("html3D.png") ## ----bga---------------------------------------------------------------------- k.bga<-bga(k.data, type="coa", classvec=k.class) ## ----BGAplot------------------------------------------------------------------ plot(k.bga, genelabels=gene.symbs) # Use the gene symbols earlier ## ----between.graph, fig.width=6, fig.height=4--------------------------------- between.graph(k.bga, ax=1) # Show the separation on the first axes(ax) ## ----CIA---------------------------------------------------------------------- # Example data are "G1_Ross_1375.txt" and "G5_Affy_1517.txt" data(NCI60) coin <- cia(NCI60$Ross, NCI60$Affy) names(coin) coin$coinertia$RV ## ----CIAplot------------------------------------------------------------------ plot(coin, classvec=NCI60$classes[,2], clab=0, cpoint=3)