lmdme-screeplot: Plot a 'screeplot' of a PCA decomposed lmdme object

In lmdme: Linear Model decomposition for Designed Multivariate Experiments

Description

Screeplot on each decomposed "pca" model present in lmdme components slot.

Usage

  ## S4 method for signature 'lmdme'
screeplot(x, independent=TRUE,
  col=seq(along=components(x)), npcs, term=NULL, mfcol,
  ...)

Arguments

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.

Value

plotted screeplot/s of the components slot if PCA decomposition was applied.

Author(s)

Cristobal Fresno and Elmer A Fernandez

See Also

stats::screeplot

Examples

{
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)
}

lmdme documentation built on Nov. 8, 2020, 7:46 p.m.