#' Get Silhouette Coefficient from (s)PCA, (s)PLS or block.(s)PLS clusters

#'

#' \code{getSilhouette} is a generic function that compute silhouette coefficient

#' for an object of the type \code{pca}, \code{spca}, \code{pls}, \code{spls},

#' \code{block.pls}, \code{block.spls}.

#'

#' @param object a mixOmics object of the class \code{pca}, \code{spca}, \code{pls}, \code{spls}, \code{block.pls}, \code{block.spls}

#'

#' @details

#' This method extract the componant contribution depending on the object,

#' perform the clustering step, and compute the silhouette coefficient.

#'

#' @return

#' silhouette coefficient

#' 

#' @examples

#' demo <- suppressWarnings(get_demo_cluster())

#' getSilhouette(object = demo$pca)

#' getSilhouette(object = demo$spca)

#' getSilhouette(object = demo$pls)

#' getSilhouette(object = demo$spls)

#' getSilhouette(object = demo$block.pls)

#' getSilhouette(object = demo$block.spls)

#' 

#'

#' @export

getSilhouette <- function(object){

    UseMethod("getSilhouette")

}

#' @importFrom magrittr %>%

#' @importFrom dplyr select

#' @export

getSilhouette.pca <- function(object){

    cluster <- getCluster(object) %>%

        dplyr::select("molecule", "cluster")

    silhouette.res <- wrapper.silhouette(X = as.data.frame(object$X), cluster = cluster$cluster)

    return(silhouette.res$average)

}

#' @importFrom magrittr %>%

#' @importFrom dplyr select

#' @export

getSilhouette.spca <- function(object){

    cluster <- getCluster(object) %>%

        dplyr::select("molecule", "cluster")

    X <- object$X %>% 

        as.data.frame() %>%

        dplyr::select(cluster$molecule)

    silhouette.res <- wrapper.silhouette(X = X, cluster = cluster$cluster)

    return(silhouette.res$average)

}

#' @export

#' @importFrom dplyr select

#' @importFrom magrittr %>%

getSilhouette.mixo_pls <- function(object){

    cluster <- getCluster(object) %>%

        dplyr::select("molecule", "cluster")

    X <- object$X %>%

        as.data.frame()

    Y <- object$Y %>%

        as.data.frame()

    data <- cbind(X,Y)

    silhouette.res <- wrapper.silhouette(X = data, cluster = cluster$cluster)

    return(silhouette.res$average)

}

#' @importFrom magrittr %>%

#' @importFrom dplyr select

#' @export

getSilhouette.mixo_spls <- function(object){

    cluster <- getCluster(object) %>%

        dplyr::select("molecule", "cluster")

    X <- object$X %>%

        as.data.frame()

    Y <- object$Y %>%

        as.data.frame()

    data <- cbind(X,Y) %>%

        dplyr::select(cluster$molecule)

    silhouette.res <- wrapper.silhouette(X = data, cluster = cluster$cluster)

    return(silhouette.res$average)

}

#' @importFrom magrittr %>%

#' @importFrom dplyr select

#' @export

getSilhouette.block.pls <- function(object){

    cluster <- getCluster(object) %>%

        dplyr::select("molecule", "cluster")

    X <- do.call("cbind", object$X) %>%

        as.data.frame

    silhouette.res <- wrapper.silhouette(X = X, cluster = cluster$cluster)

    return(silhouette.res$average)

}

#' @importFrom magrittr %>%

#' @importFrom dplyr select

#' @export

getSilhouette.block.spls <- function(object){

    cluster <- getCluster(object) %>%

        dplyr::select("molecule", "cluster")

    X <- do.call("cbind", object$X) %>%

        as.data.frame %>%

        dplyr::select(cluster$molecule)

    silhouette.res <- wrapper.silhouette(X = X, cluster = cluster$cluster)

    return(silhouette.res$average)

}