R/plotDesign.R

In PeteHaitch/RUVcorr: Removal of unwanted variation for gene-gene correlations and related analysis.

#' Plot nested design structure.
#' 
#' \code{plotDesign} returns a plot with different color strips representing
#' different factors relating to the study design.
#' genes.
#' 
#' @param anno A dataframe or matrix containing the annotation of the study.
#' @param Factors A vector of factors that should be plotted.
#' @param anno.names A vector containing the names, the default \code{Factors}. 
#' @param orderby A character describing an element in \code{Factor} by which the 
#' 	data should be ordered.
#' @return \code{plotDesign} returns a plot.
#' 
#' @examples
#' data(ColantuoniAnnotation)
#' plotDesign(ColantuoniAnnotation, c("Brain_Bank_Source", "Array_Batch"))
#' @author Saskia Freytag
#' @export
plotDesign<-function(	anno, 
		Factors, 
		anno.names=Factors, 
		orderby=NULL){
		
	#testing
	if(any(is.element(Factors,colnames(anno))==FALSE)) stop("Factors need to be in anno.")
	if(is.null(orderby)==FALSE){
	if(is.element(orderby, colnames(anno))==FALSE) stop("orderby need to be in anno.")
	}
	if(length(Factors)!=length(anno.names)) warning("Not enough names specified in anno.names.")
	
	if(is.null(orderby)==FALSE){
		tmp<-which(is.element(colnames(anno), orderby))
		Order<-order(as.factor(anno[,tmp]))
		anno<-anno[Order,]
	}
	extract<-vector()
	for(i in Factors){
		extract<-c(extract, which(colnames(anno)==i))
	}
	anno<-anno[,extract]
	a<-dim(anno)[1]

	par(mfrow=c(dim(anno)[2],1), mar=c(1,2,0.5,1), mgp=c(0.5, 1, 0))

	for(i in 1:length(anno.names)){
		x<-anno[,i]
		x.name<-anno.names[i]
		x<-as.numeric(as.factor(x))
		n.category<-length(unique(x))
		colors<-hcl(h = seq(0,360,round(360/n.category,2))[1:n.category], c=45, l=70)
		#colors<-colors[sample(1:length(colors),length(colors))]
		image(seq(0,a*0.1, 0.1)[1:a],y=1, as.matrix(x), col=colors,
		axes=FALSE, ylab=paste(x.name), xlab="", cex=3)
	}

}