lmdme-loadingplot: 'loadingplot' of interaction PCA decomposed lmdme object
In lmdme: Linear Model decomposition for Designed Multivariate Experiments

Description Usage Arguments Value Author(s) Examples

This function plots the PCA loadings for a given interaction (A:B) lmdme object's components slot, for the given "pc" component. The user can choose which term (A or B) is used for x-axis and y-axis functions (B or A) respectively.

1
2
3

  ## S4 method for signature 'lmdme'
loadingplot(object, term.x, term.y,
  pc=1, ord.x, col, ...)

`object`	lmdme class object.
`term.x,term.y`	character indicating the model principal factor for the interaction term (term.x:term.y or term.y:term.x) for the corresponding x or y axis.
`pc`	integer indicating which principal component loading is to be plotted on the y-axis. Default value is 1.
`col`	which color to use for each level present in term.y.
`ord.x`	numeric indicating the term.x levels order, for plotting purposes. If missing, the levels order is used.
`...`	additional parameters for matplot.

loading plot of the selected interaction (term.x:term.y) lmdme object's components slot, if PCA decomposition was applied.

Cristobal Fresno and Elmer A Fernandez

{
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: 
loadingplot(fit, term.x="time", term.y="oxygen")

##Or change the axis order
loadingplot(fit, term.x="oxygen", term.y="time")

##Or change the PC to display
loadingplot(fit, term.x="time", term.y="oxygen", pc=2)

##Or the order of x-levels
loadingplot(fit, term.x="time", term.y="oxygen", ord.x=3:1)

## End(Not run)
}