R/visual-cluster-in-bipartite.R

In jafarilab/NIMAA: Nominal Data Mining Analysis

#' Plot the bipartite graph with color coding for different clusters in both parts
#'
#' @description The Sankey diagram is used to depict the connections between clusters within each part of the bipartite network. The display is also interactive, and by grouping nodes within each cluster as "summary" nodes, this function emphasizes how clusters of each part are connected together.
#'
#' @param data A data frame or matrix object as an edge list.
#' @param community_left An igraph community object, one projection of the bipartite network to be showed on the left side.
#' @param community_right An igraph community object, the other projection of the bipartite network to be showed on the right side.
#' @param name_left A string value, the name of left community.
#' @param name_right A string value, the name of right community.
#'
#' @return A customized Sankey plot with a data frame containing the cluster pairwise relationship with the sum of weight values in the weighted bipartite network.
#' @seealso \code{\link[plotly]{plot_ly}}
#'
#' @importFrom  dplyr inner_join group_by summarize
#' @import RColorBrewer
#' @export
#'
#' @examples
#' # load part of the beatAML data
#' beatAML_data <- NIMAA::beatAML[1:1000,]
#'
#' # convert to incidence matrix
#' beatAML_incidence_matrix <- nominalAsBinet(beatAML_data)
#'
#' # extract the Recetengular_element_max submatrix
#' sub_matrices <- extractSubMatrix(beatAML_incidence_matrix,
#' col.vars = "patient_id", row.vars = "inhibitor",
#' shape = c("Rectangular_element_max"))
#'
#' # do clustering analysis
#' cls1 <- findCluster(sub_matrices$Rectangular_element_max,
#' part = 1, comparison = FALSE)
#'
#' cls2 <- findCluster(sub_matrices$Rectangular_element_max,
#' part = 2, comparison = FALSE)
#'
#' visualClusterInBipartite(data = beatAML_data,
#' community_left = cls2$leading_eigen,
#' community_right = cls1$fast_greedy,
#' name_left = 'patient_id',
#' name_right = 'inhibitor')
visualClusterInBipartite <- function(data,
                                     community_left,
                                     community_right,
                                     name_left = "Left",
                                     name_right  = "Right") {
  # to avoid devtools::check() notes... meaningless
  group_left <- group_right <- value <- NULL

  group_mapping_list_left <- data.frame(group_left = paste0(name_left, " Group ",community_left$membership), node = community_left$names)
  group_mapping_list_right <- data.frame(group_right = paste0(name_right, " Group ",community_right$membership), node = community_right$names)

  data_cn <- colnames(data)
  colnames(data) <- c("var1", "var2", "value")

  if (FALSE %in% (data[,'var1'] %in% group_mapping_list_left[,'node'])) {
    colnames(data) <- c("var2", "var1", "value")
  }
  print_df <- dplyr::inner_join(data, group_mapping_list_left, by = c("var1" = "node")) %>%
    dplyr::inner_join(y = group_mapping_list_right, by = c("var2" = "node")) %>%
    dplyr::group_by(group_left, group_right) %>%
    dplyr::summarize(value = sum(value), .groups = "keep")

  left_df <-  dplyr::group_by(print_df, group_left)%>%
    dplyr::summarize(value = sum(value), .groups = "keep")
  right_df <-  dplyr::group_by(print_df, group_right)%>%
    dplyr::summarize(value = sum(value), .groups = "keep")

  node_number_left <- table(group_mapping_list_left[, "group_left"])
  node_number_right <- table(group_mapping_list_right[, "group_right"])
  customdata <- paste(c(node_number_left, node_number_right, "node(s)"))

  after_rank_left <- match(node_number_left, sort(unique(node_number_left)))
  after_rank_right <- match(node_number_right, sort(unique(node_number_right)))
  node_colors <- c(RColorBrewer::brewer.pal(n=3,name='Blues')[after_rank_left],RColorBrewer::brewer.pal(n=3,name='PuRd')[after_rank_left])
  fig <- plotly::plot_ly(
    type = "sankey",
    orientation = "h",
    arrangement = "perpendicular",
    node = list(
      label = c(unique(print_df$group_left), unique(print_df$group_right)),
      customdata = customdata,
      pad = 15,
      thickness = 20,
      color = node_colors,
      line = list(
        color = "black",
        width = 0.5
      ),
      hovertemplate = "%{customdata}"
    ),
    link = list(
      source = as.integer(factor(print_df$group_left, labels = "")) - 1,
      target = as.integer(factor(print_df$group_right, labels = "")) + length(unique(print_df$group_left)) - 1,
      value = print_df$value,
      label = as.character(interaction(print_df[, c("group_left", "group_right")], sep = "<-->")),
      hovertemplate = "%{label}"
    )
  )
  print(fig)
  return(print_df)
}