#' Plot feature importance bar graph
#'
#' Read a data.table containing feature importance details and plot it (for both GLM and Trees).
#'
#' @importFrom magrittr %>%
#' @param importance_matrix a \code{data.table} returned by the \code{xgb.importance} function.
#' @param numberOfClusters a \code{numeric} vector containing the min and the max range of the possible number of clusters of bars.
#'
#' @return A \code{ggplot2} bar graph representing each feature by a horizontal bar. Longer is the bar, more important is the feature. Features are classified by importance and clustered by importance. The group is represented through the color of the bar.
#'
#' @details
#' The purpose of this function is to easily represent the importance of each feature of a model.
#' The function returns a ggplot graph, therefore each of its characteristic can be overriden (to customize it).
#' In particular you may want to override the title of the graph. To do so, add \code{+ ggtitle("A GRAPH NAME")} next to the value returned by this function.
#'
#' @examples
#' data(agaricus.train, package='xgboost')
#'
#' #Both dataset are list with two items, a sparse matrix and labels
#' #(labels = outcome column which will be learned).
#' #Each column of the sparse Matrix is a feature in one hot encoding format.
#'
#' bst <- xgboost(data = agaricus.train$data, label = agaricus.train$label, max.depth = 2,
#'                eta = 1, nthread = 2, nround = 2,objective = "binary:logistic")
#'
#' #agaricus.train$data@@Dimnames[[2]] represents the column names of the sparse matrix.
#' importance_matrix <- xgb.importance(agaricus.train$data@@Dimnames[[2]], model = bst)
#' xgb.plot.importance(importance_matrix)
#'
#' @export
xgb.plot.importance <-
  function(importance_matrix = NULL, numberOfClusters = c(1:10)) {
    if (!"data.table" %in% class(importance_matrix))  {
      stop("importance_matrix: Should be a data.table.")
    }
    if (!requireNamespace("ggplot2", quietly = TRUE)) {
      stop("ggplot2 package is required for plotting the importance", call. = FALSE)
    }
    if (!requireNamespace("Ckmeans.1d.dp", quietly = TRUE)) {
      stop("Ckmeans.1d.dp package is required for plotting the importance", call. = FALSE)
    }
    
    if(isTRUE(all.equal(colnames(importance_matrix), c("Feature", "Gain", "Cover", "Frequency")))){
      y.axe.name <- "Gain"
    } else if(isTRUE(all.equal(colnames(importance_matrix), c("Feature", "Weight")))){
      y.axe.name <- "Weight"
    } else {
      stop("Importance matrix is not correct (column names issue)")
    }
    
    # To avoid issues in clustering when co-occurences are used
    importance_matrix <-
      importance_matrix[, .(Gain.or.Weight = sum(get(y.axe.name))), by = Feature]
    
    clusters <-
      suppressWarnings(Ckmeans.1d.dp::Ckmeans.1d.dp(importance_matrix[,Gain.or.Weight], numberOfClusters))
    importance_matrix[,"Cluster":= clusters$cluster %>% as.character]
    
    plot <-
      ggplot2::ggplot(
        importance_matrix, ggplot2::aes(
          x = stats::reorder(Feature, Gain.or.Weight), y = Gain.or.Weight, width = 0.05
        ), environment = environment()
      ) + ggplot2::geom_bar(ggplot2::aes(fill = Cluster), stat = "identity", position =
                              "identity") + ggplot2::coord_flip() + ggplot2::xlab("Features") + ggplot2::ylab(y.axe.name) + ggplot2::ggtitle("Feature importance") + ggplot2::theme(
                                plot.title = ggplot2::element_text(lineheight = .9, face = "bold"), panel.grid.major.y = ggplot2::element_blank()
                              )
    
    return(plot)
  }

# Avoid error messages during CRAN check.
# The reason is that these variables are never declared
# They are mainly column names inferred by Data.table...
globalVariables(
  c(
    "Feature", "Gain.or.Weight", "Cluster", "ggplot", "aes", "geom_bar", "coord_flip", "xlab", "ylab", "ggtitle", "theme", "element_blank", "element_text", "Gain.or.Weight"
  )
)