screeplot {lmdme} | R Documentation |
screeplot
of a PCA decomposed lmdme objectScreeplot on each decomposed "pca" model present in lmdme components slot.
## S4 method for signature 'lmdme' screeplot(x, independent=TRUE, col=seq(along=components(x)), npcs, term=NULL, mfcol, ...)
x |
lmdme class object. |
independent |
logical indicating whether the screeplots should be plotted together. Default value is FALSE. |
col |
which color to use for each decomposed model. Default value seq(along= components(x)). |
npcs |
integer with the number of components to plot. By default all present components are plotted. |
term |
character with the corresponding term/s for biploting. Default value is NULL in order to obtain every available biplot/s. |
mfcol |
numeric vector for par layout. If missing, mfcol=c(1,2) will be used if more than one biplot is available. Use mfcol==NULL to override par call inside biplot function. |
... |
additional parameters for screeplot or plot/lines according to independent FALSE or TRUE respectively. |
plotted screeplot/s of the components slot if PCA decomposition was applied.
Cristobal Fresno and Elmer A Fernandez
stats::screeplot
{ data(stemHypoxia) ##Just to make a balanced dataset in the Fisher sense (2 samples per ## time*oxygen levels) design<-design[design$time %in% c(0.5,1,5) & design$oxygen %in% c(1,5,21), ] design$time <-as.factor(design$time) design$oxygen<-as.factor(design$oxygen) rownames(M)<-M[, 1] #Keeping appropriate samples only M<-M[, colnames(M) %in% design$samplename] ##ANOVA decomposition fit<-lmdme(model=~time+oxygen+time:oxygen, data=M, design=design) ##ASCA for all the available terms, on those subjects/genes where at least ##one interaction coefficient is statistically different from zero (F-test ##on the coefficients). id<-F.p.values(fit,term="time:oxygen")<0.001 decomposition(fit, decomposition="pca", scale="row", subset=id) ## Not run: par(mfrow=c(2,2)) ##Does not call par inside screeplot(fit,mfcol=NULL) ##Just the term of interest screeplot(fit,term="time") ##In separate graphics screeplot(fit,term=c("time","oxygen"),mfcol=c(1,1)) ##All term in the same graphic device screeplot(fit,mfcol=c(1,3)) ##All in the same graphic screeplot(fit,independent=FALSE) ## End(Not run) }