--- a
+++ b/R/plotLong.R
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+#' 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))
+}