MApckg: R package of MetaboAnalyst functions

#' EBAM Fudge Factor
#'
#' \code{EBAM.A0.Anal} - finds EBAM Fudge Factor. Uses \code{\link[siggenes]{find.a0}} function.
#'
#' @return \code{EBAM.A0.Anal} - native \code{analSet} with one added \code{$ebam.a0} element containing 
#' standard \code{\link[siggenes]{find.a0}} function output
#' @describeIn EBAM.Anal Find EBAM Fudge Factor.
#' @export

# deteriming a0, only applicable for z.ebam (default)
EBAM.A0.Anal<-function(dataSet, analSet, paired=FALSE, var.equal=TRUE){

    if(paired){
        cl.ebam<-as.numeric(dataSet$pairs); 
    }else{
        cl.ebam<-as.numeric(dataSet$cls)-1; # change to 0 and 1 for class label
    }
    conc.ebam<-t(dataSet$norm); # in sam column is sample, row is gene
    ebam_a0<-siggenes::find.a0(conc.ebam, cl.ebam, var.equal=var.equal, gene.names = names(dataSet$norm), rand=123);
	analSet$ebam.a0<-ebam_a0;
	return(analSet);
}

#' EBAM analysis
#'
#' \code{EBAM.Cmpd.Anal} - performs Empirical Bayesian Analysis of Microarray (and Metabolites).
#' Uses \code{\link[siggenes]{ebam}} function.
#'
#' @param dataSet List, data set object generated by \code{\link[MSdata]{MS_to_MA}} function.
#' @param analSet List, containing the results of statistical analysis (can be just an empty list).
#' @param method A character string or name specifying the method or function
#' that should be used in the computation of the expression score z.
#' If \code{"z.ebam"}, a modified t- or F-statistic, respectively, will be computed as proposed by Efron et al. (2001).
#' If \code{"wilc.ebam"}, a (standardized) Wilcoxon sum / signed rank statistic will be used as expression score.
#' Note: if method is \code{"wilc.ebam"}, then \code{A0} and \code{var.equal} parameters will be ignored
#' @param A0 Fudge Factor. \code{\link{EBAM.A0.Anal}}
#' @param paired Are values in data set paired or not.
#' @param var.equal Are variances assumed equal or not.
#' @return \code{EBAM.Cmpd.Anal} - native \code{analSet} with one added \code{$ebam} element containing 
#' standard \code{\link[siggenes]{ebam}} function output
#' @seealso \code{\link[siggenes]{ebam}}, \code{\link[siggenes]{find.a0}} for used statistical functions\cr
#' \code{\link{SetEBAMSigMat}} for setting matrix of significance\cr
#' \code{\link{PlotEBAM}} for plotting functions
#' @rdname EBAM.Anal
#' @export
# note: if method is wilcoxon, the A0 and var equal will be ignored
EBAM.Cmpd.Anal<-function(dataSet, analSet, method="z.ebam", A0=0, paired=FALSE, var.equal=TRUE){
    match.arg(method, c("z.ebam", "wilc.ebam"))
	if(paired){
        cl.ebam<-as.numeric(dataSet$pairs);
    }else{
        cl.ebam<-as.numeric(dataSet$cls)-1;
    }
    conc.ebam<-t(dataSet$norm); # in sam column is sample, row is feature
    if(method=="z.ebam"){
        ebam_out<-siggenes::ebam(conc.ebam, cl.ebam, method="z.ebam", a0=A0, var.equal=var.equal, fast=TRUE, gene.names = names(dataSet$norm), rand=123);
    }else{
        ebam_out<-siggenes::ebam(conc.ebam, cl.ebam, method="wilc.ebam", gene.names = names(dataSet$norm), rand=123);
    }
    analSet$ebam<-ebam_out;
	return(analSet);
}

#' EBAM matrix of significance
#'
#' EBAM matrix of significance. Writes results to \code{"ebam_sigfeatures.csv"} file.
#'
#' @param dataSet List, data set object generated by \code{\link[MSdata]{MS_to_MA}} function.
#' @param analSet List, containing the results of statistical analysis (can be just an empty list).
#' @param delta The delta to control FDR
#' @return Native \code{analSet} with two added elements:
#' \itemize{
#' \item\code{$ebam.cmpd} - matrix containing \code{z.value}, \code{posterior}, \code{local.fdr} columns
#' \item\code{$ebam.delta} - value of \code{delta} argument
#' }
#' @export
#' @seealso \code{\link{EBAM.Anal}} for analytical function\cr
#' \code{\link{PlotEBAM}} for plotting functions
# return double matrix with 3 columns - z.value, posterior, local.fdr
SetEBAMSigMat<-function(dataSet, analSet, delta=0.9){
    ebam.sum<-summary(analSet$ebam, delta);
    summary.mat<-ebam.sum@mat.sig;
    sig.mat <-as.matrix(signif(summary.mat[,-1],5));
    write.csv(signif(sig.mat,5),file="ebam_sigfeatures.csv");
    analSet$ebam.cmpds<-sig.mat;
    analSet$ebam.delta<-delta;
	return(analSet);
}


#' Plot EBAM
#'
#' Functions for plotting the results of EBAM.
#'
#' @param dataSet List, data set object generated by \code{\link[MSdata]{MS_to_MA}} function.
#' @param analSet List, containing the results of statistical analysis (can be just an empty list). 
#' @param imgName Image file name prefix.
#' @param format Image format, one of: "png", "tiff", "pdf", "ps", "svg"
#' @param dpi Image resolution.
#' @param width Image width.
#' @seealso \code{\link{EBAM.Anal}}, \code{\link{SetEBAMSigMat}} for analytical functions
#' @name PlotEBAM
NULL

#' \code{PlotEBAM.A0} - plot EBAM A0 plot.
#' @rdname PlotEBAM
#' @export
# plot ebam a0 plot also return the analSet$ebam.a0 object so that the suggested a0 can be obtained
PlotEBAM.A0<-function(dataSet, analSet, imgName="ebam_view_", format="png", dpi=72, width=NA){
    if (is.null(analSet$ebam.a0)) stop("Please, conduct EBAM.A0.Anal first.")
	
	imgName = paste(imgName, "dpi", dpi, ".", format, sep="");
    if(is.na(width)){
        w <- 8;
    }else if(width == 0){
        w <- 7; 
        analSet$imgSet$ebam.a0<-imgName;
    }
    h <- 3*w/4;
    Cairo::Cairo(file = imgName, unit="in", dpi=dpi, width=w, height=h, type=format, bg="white");
	plot(analSet$ebam.a0);
    dev.off();
	frame()
	grid::grid.raster(png::readPNG(imgName));
}

#' \code{PlotEDAM.Cmpd} - plot significant features.
#' @rdname PlotEBAM
#' @export
# plot ebam
PlotEBAM.Cmpd<-function(dataSet, analSet, imgName="ebam_imp_", format="png", dpi=72, width=NA){
	if (is.null(analSet$ebam)) stop("Please, conduct EBAM.Cmpd.Anal and SetEBAMSigMat first.")
	if (is.null(analSet$ebam.cmpds)) stop("Please, conduct SetEBAMSigMat first.")
    
	imgName = paste(imgName, "dpi", dpi, ".", format, sep="");
    if(is.na(width)){
        w <- h <- 7;
    }else if(width == 0){
        w <- h <- 7;
        analSet$imgSet$ebam.cmpd<-imgName;
    }else{
        w <- h <- width;
    }
    Cairo::Cairo(file = imgName, unit="in", dpi=dpi, width=w, height=h, type=format, bg="white");
	plot(analSet$ebam, analSet$ebam.delta);
    dev.off();
	frame()
	grid::grid.raster(png::readPNG(imgName));
}

GetEBAMSigMat<-function(analSet){
    return(CleanNumber(analSet$ebam.cmpds));
}

GetEBAMSigRowNames<-function(analSet){
    rownames(analSet$ebam.cmpds);
}

GetEBAMSigColNames<-function(analSet){
    colnames(analSet$ebam.cmpds);
}

GetSigTable.EBAM<-function(dataSet, analSet){
    GetSigTable(dataSet, analSet$ebam.cmpds, "EBAM");
}