loadingplot {lmdme} | R Documentation |
loadingplot
of interaction PCA decomposed lmdme objectThis 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.
## 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) }