R/optimize.R

In RnaSeqSampleSize: RnaSeqSampleSize

# TODO: Add comment
# 
# Author: zhaos
###############################################################################

##' optimize_parameter
##' 
##' A function to optimize the parameters in power or sample size estimation.
##' 
##' A function to optimize the parameters in power or sample size estimation.
##' 
##' @param fun function to be optimized, can be est_power, sample_size.
##' @param opt1 parameter1 to be optimized.
##' @param opt2 parameter2 to be optimized.
##' @param opt1Value values of parameter1 to be optimized.
##' @param opt2Value values of parameter2 to be optimized.
##' @param main Title of optimization result figure.
##' @param ... Other parameters for optimized funtion.
##' @importFrom heatmap3 heatmap3
##' @importFrom matlab jet.colors
##' @return A power or sample size matrix, generated by different pair of two paramters.
##' @export
##' @examples #Optimization for power estimation
##' result<-optimize_parameter(fun=est_power,opt1="n",opt2="lambda0",opt1Value=c(3,5,10,15,20),opt2Value=c(1:5,10,20))
##' #Optimization for sample size estimation
##' result<-optimize_parameter(fun=sample_size,opt1="lambda0",opt2="phi0",opt1Value=c(1,3),opt2Value=c(1.5,2),power=0.8)
optimize_parameter<-function(fun=est_power,opt1,opt2,opt1Value,opt2Value,main,...){
	if (missing(main)) {
		if (identical(fun,est_power)) {
			main<-"Optimization for Power Estimation"
		} else if (identical(fun,sample_size)) {
			main<-"Optimization for Sample Size Estimation"
		} else {
			main<-"Optimization"
		}
	}
	argList<-list(...)
	result<-NULL
	for (opt1ValueEach in opt1Value) {
		for (opt2ValueEach in opt2Value) {
			argList[[opt1]]<-opt1ValueEach
			argList[[opt2]]<-opt2ValueEach
			result<-c(result,do.call(fun,argList))
		}
	}
	result<-matrix(result,ncol=length(opt1Value))
	colnames(result)<-opt1Value
	row.names(result)<-opt2Value
#	heatmap3(result,Colv=NA,Rowv=NA,xlab=opt1,ylab=opt2,scale="n",col=heat.colors(1024),cexCol=1,cexRow=1,las=1,main=main)
	heatmap3(result,Colv=NA,Rowv=NA,xlab=opt1,ylab=opt2,scale="n",col=matlab::jet.colors(1000),cexCol=1,cexRow=1,lasCol=1,lasRow=1,main=main)
	return(result)
}