#' Plot Longitudinal Profiles by Cluster

#'

#' This function provides a expression profile representation over time and by cluster.

#'

#' @param object a mixOmics result of class (s)pca, (s)pls, block.(s)pls.

#' @param time (optional) a numeric vector, the same size as \code{ncol(X)}, to change the time scale.

#' @param plot a logical, if TRUE then  a plot is produced. Otherwise, the data.frame on which the plot is based on is returned.

#' @param center a logical value indicating whether the variables should be shifted to be zero centered. 

#' @param scale a logical value indicating whether the variables should be scaled to have unit variance before the analysis takes place. 

#' @param title character indicating the title plot.

#' @param X.label x axis titles.

#' @param Y.label y axis titles.

#' @param legend a logical, to display or not the legend.

#' @param legend.title if \code{legend} is provided, title of the legend.

#' @param legend.block.name a character vector corresponding to the size of the number of blocks in the mixOmics object. 

#' 

#'

#' @return

#' a data.frame (gathered form) containing the following columns:

#' \item{time}{x axis values}

#' \item{molecule}{names of features}

#' \item{value}{y axis values}

#' \item{cluster}{assigned clusters}

#' \item{block}{name of 'blocks'}

#' 

#' @seealso 

#' \code{\link[timeOmics]{getCluster}}

#'

#' @examples

#' demo <- suppressWarnings(get_demo_cluster())

#' X <- demo$X

#' Y <- demo$Y

#' Z <- demo$Z

#' 

#' # (s)pca

#' pca.res <- mixOmics::pca(X, ncomp = 3)

#' plotLong(pca.res)

#' spca.res <- mixOmics::spca(X, ncomp =2, keepX = c(15, 10))

#' plotLong(spca.res)

#' 

#' # (s)pls

#' pls.res <- mixOmics::pls(X,Y)

#' plotLong(pls.res)

#' spls.res <- mixOmics::spls(X,Y, keepX = c(15,10), keepY=c(5,6))

#' plotLong(spls.res)

#' 

#' # (s)block.spls

#' block.pls.res <- mixOmics::block.pls(X=list(X=X,Z=Z), Y=Y)

#' plotLong(block.pls.res)

#' block.spls.res <- mixOmics::block.spls(X=list(X=X,Z=Z), Y=Y, 

#'                              keepX = list(X = c(15,10), Z = c(5,6)), 

#'                              keepY = c(3,6))

#' plotLong(block.spls.res)

#' 

#'

#' @import ggplot2

#' @import mixOmics

#' @importFrom tibble rownames_to_column

#' @importFrom dplyr mutate select left_join

#' @importFrom tidyr pivot_longer

#' @export

plotLong <- function(object, time = NULL, plot = TRUE, center = TRUE, scale = TRUE, 

                     title="Time-course Expression", X.label=NULL, Y.label=NULL, 

                     legend=FALSE, legend.title=NULL, legend.block.name = NULL)

{

    # Check parameters

    #-- object

    allowed_object = c("pca", "spca", "mixo_pls", "mixo_spls", "block.pls", "block.spls")

    if(!any(class(object) %in% allowed_object)){

        stop("invalid object, should be one of c(pca, spca, mixo_pls, mixo_spls, block.pls, block.spls)")

    }

    #-- plot : if plot is not correct, plot = FALSE

    if(is.null(plot)) plot = FALSE

    if(!is.finite(plot) || !is.logical(plot)){plot = FALSE}

    #-- center

    if(is.null(center)) center = TRUE

    if(!is.finite(center) || !is.logical(center)){center = TRUE}

    #-- scale

    if(is.null(scale)) scale = TRUE

    if(!is.finite(scale) || !is.logical(scale)){scale = TRUE}

    # graphical options

    #-- title

    if(!is.character(title)){title = NULL}

    #-- X.label

    if(!is.character(X.label)){X.label = NULL}

    #-- Y.label

    if(!is.character(Y.label)){Y.label = NULL}

    #-- legend

    if(is.null(legend)) legend = FALSE

    if(!is.finite(legend) || !is.logical(legend)){legend = FALSE}

    #-- legend title

    if(!is.character(legend.title)){legend.title = NULL}

    # cluster info

    cluster <- getCluster(object)

    #-- legend.block.name

    if(!is.null(legend.block.name)){

        check_legend.block.name(legend.block.name, cluster)

        new.block.name.tmp <- list(new.block = legend.block.name, block = unique(cluster$block)) %>%

            as.data.frame

        cluster <- cluster %>% left_join(new.block.name.tmp, by = c("block"="block")) %>%

            mutate(old.block = block, block = new.block) %>% 

            dplyr::select(-new.block)

    }

    if(is(object, "pca") || is(object, "spca")){

        #-- check time

        if(!is.null(time) && (!is_almostInteger_vector(time) || (length(time) != nrow(object$X)))){

            stop("'time' should be a numeric vector")

        }

        # scale/unscale if desired

        data <- unscale(object$X) %>%

            as.data.frame() %>%

            dplyr::select(intersect(cluster$molecule, colnames(.))) %>%

            scale(scale, center)

    } else if(is(object, "mixo_pls") || is(object, "mixo_spls")){

        #-- check time

        if(!is.null(time) && (!is_almostInteger_vector(time) || (length(time) != nrow(object$X)))){

            stop("'time' should be a numeric vector")

        }

        data.X <- unscale(object$X) %>%

            scale(scale, center)

        data.Y <- unscale(object$Y) %>%

            scale(scale, center)

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

            as.data.frame() %>%

            dplyr::select(intersect(cluster$molecule, colnames(.)))

    } else if(is(object, "block.pls") || is(object, "block.spls")){

        #-- check time

        if(!is.null(time) &&(!is_almostInteger_vector(time) || (length(time) != nrow(object$X[[1]])))){

            stop("'time' should be a numeric vector")

        }

        data <- lapply(object$X, function(i){unscale(i) %>%

                scale(scale, center)}) %>% 

            do.call(what = "cbind")

        data <- as.data.frame(data) %>% 

            dplyr::select(intersect(cluster$molecule, colnames(.)))

    }

    # plot

    if(!is.null(time)){

        rownames(data) <- time   

    }

    data.gather <- data %>%

        as.data.frame() %>% 

        tibble::rownames_to_column("time") %>%

        dplyr::mutate(time = as.numeric(.$time)) %>%

        tidyr::pivot_longer(names_to = "molecule", values_to = "value", -time) %>%

        dplyr::left_join(cluster, by = c("molecule"="molecule")) %>%

        dplyr::mutate(block = factor(block))

    gg <- ggplot(data.gather, aes(x = time, y = value, group = molecule)) +

        geom_line(aes(color = block)) +

        facet_grid(contribution ~ comp, scales = "free") +

        scale_color_manual(values = mixOmics::color.mixo(1:length(levels(data.gather$block)))) +

        theme_bw() 

    if(is.character(title)){

        gg <- gg + ggtitle(title)

    }

    if(!is.null(X.label)){

        gg <- gg + xlab(X.label)

    } else {

        gg <- gg + xlab("Time")

    }

    if(!is.null(Y.label)){

        gg <- gg + ylab(Y.label)

    } else {

        gg <- gg + ylab("Expression")

    }

    if(!legend){

        gg <- gg + theme(legend.position = "none")

    } else { # legend is TRUE

        if(!is.null(legend.title)){

            gg <- gg + labs(color = legend.title)

        }

    }

    if(plot){

        print(gg)

    }

    return(invisible(gg$data))

}