methods-coercion.r

#' @include diffusionmap.r dpt.r
NULL

#' Coercion methods
#' 
#' Convert a \code{\link{DiffusionMap}} or \code{\link{DPT}} object to other classes
#' 
#' \link[ggplot2]{fortify} is a ggplot2 generic allowing a diffusion map to be used as \code{data} parameter in \link[ggplot2]{ggplot} or \link[ggplot2]{qplot}. 
#' 
#' @param x,model  A \code{\link{DiffusionMap}} or \code{\link{DPT}} object
#' @param row.names  NULL or a character vector giving the row names for the data frame. Missing values are not allowed.
#' @param optional  logical. If TRUE, setting row names and converting column names (to syntactic names: see make.names) is optional.

#' @param ...  Passed to \code{\link[base]{as.data.frame}}
#' @param data  ignored
#' 
#' @return An object of the desired class
#' 
#' @seealso \link{DiffusionMap accession methods}, \link{Extraction methods}, \link{DiffusionMap methods} for more
#' 
#' @examples
#' library(Biobase)
#' data(guo)
#' dm <- DiffusionMap(guo)
#' classes <- vapply(as.data.frame(dm), class, character(1L))
#' stopifnot(all(classes[paste0('DC', 1:20)] == 'numeric'))
#' stopifnot(all(classes[featureNames(guo) ] == 'numeric'))
#' stopifnot(all(classes[   varLabels(guo) ] == c('factor', 'integer')))
#' 
#' @aliases
#' as.data.frame.DiffusionMap fortify.DiffusionMap
#' as.data.frame.DPT          fortify.DPT
#'     as.matrix.DPT
#' 
#' @importFrom methods setAs
#' @importFrom BiocGenerics as.data.frame
#' @name Coercion methods
#' @rdname coercions
#' @include diffusionmap.r
NULL


#' @importFrom Biobase pData
#' @rdname coercions
#' @export
setMethod('as.data.frame', 'DiffusionMap', function(x, row.names = NULL, optional = FALSE, ...) {
	df_evec <- as.data.frame(eigenvectors(x), row.names, optional, ...)
	df_data <- dataset_to_df(     dataset(x), row.names, optional, ...)
	
	if (is.null(df_data))
		df_evec
	else
		cbind(df_evec, df_data)
})


#' @usage fortify.DiffusionMap(model, data, ...)
#' 
#' @importFrom BiocGenerics as.data.frame
#' @importFrom Biobase as.data.frame.ExpressionSet
#' @importFrom ggplot2 fortify
#' @rdname coercions
#' @exportS3Method fortify DiffusionMap
#' @export fortify.DiffusionMap
fortify.DiffusionMap <- function(model, data, ...) as.data.frame(model, ...)
setAs('DiffusionMap', 'data.frame', function(from) as.data.frame(from))


#' @rdname coercions
#' @export
setMethod('as.data.frame', 'DPT', function(x, row.names = NULL, optional = FALSE, ...) {
	dpt <- as.matrix(x)
	colnames(dpt) <- paste0('DPT', seq_len(ncol(dpt)))
	cbind(
		as.data.frame(cbind(dpt, x@branch, x@tips), row.names = row.names, optional = optional, ...),
		as.data.frame(x@dm,                         row.names = row.names, optional = optional, ...))
})


#' @usage fortify.DPT(model, data, ...)
#' 
#' @importFrom BiocGenerics as.data.frame
#' @importFrom Biobase as.data.frame.ExpressionSet
#' @importFrom ggplot2 fortify
#' @rdname coercions
#' @exportS3Method fortify DPT
#' @export fortify.DPT
fortify.DPT <- function(model, data, ...) as.data.frame(model, ...)
setAs('DPT', 'data.frame', function(from) as.data.frame(from))


#' @rdname coercions
#' @export
setMethod('as.matrix', 'DPT', function(x, ...) x[])