R/visualize_parent_nebula.R

In Cao-lab-zcmu/MCnebula: MCnebula algorithm integration in R

#' @title FUNCTION_TITLE
#' @description FUNCTION_DESCRIPTION
#' @param graph PARAM_DESCRIPTION, Default: .MCn.parent_graph
#' @param write_output PARAM_DESCRIPTION, Default: T
#' @param output PARAM_DESCRIPTION, Default: paste0(.MCn.output, "/", .MCn.results)
#' @param layout PARAM_DESCRIPTION, Default: 'mds'
#' @param nodes_color PARAM_DESCRIPTION, Default: c(hierarchy = 4)
#' @param width PARAM_DESCRIPTION, Default: 15
#' @param height PARAM_DESCRIPTION, Default: 12
#' @param return_plot PARAM_DESCRIPTION, Default: F
#' @param ... PARAM_DESCRIPTION
#' @return OUTPUT_DESCRIPTION
#' @details DETAILS
#' @examples 
#' \dontrun{
#' if(interactive()){
#'  #EXAMPLE1
#'  }
#' }
#' @seealso 
#'  \code{\link[pbapply]{pbapply}}
#'  \code{\link[data.table]{rbindlist}}
#'  \code{\link[dplyr]{select}}, \code{\link[dplyr]{rename}}, \code{\link[dplyr]{mutate}}, \code{\link[dplyr]{reexports}}
#'  \code{\link[tidygraph]{as_tbl_graph.data.frame}}, \code{\link[tidygraph]{activate}}
#'  \code{\link[ggraph]{ggraph}}
#'  \code{\link[ggplot2]{ggsave}}
#' @rdname visualize_parent_nebula
#' @export 
#' @importFrom pbapply pblapply
#' @importFrom data.table rbindlist
#' @importFrom dplyr select rename mutate as_tibble
#' @importFrom tidygraph as_tbl_graph activate tbl_graph
#' @importFrom ggraph create_layout
#' @importFrom ggplot2 ggsave
visualize_parent_nebula <-
  function(
           graph = .MCn.parent_graph,
           write_output = T,
           output = paste0(.MCn.output, "/", .MCn.results),
           layout = "mds",
           nodes_color = c("hierarchy" = 3), ## default, use superclass as color.
           width = 15,
           height = 12,
           return_plot = F,
           ...
           ){
    cat("[INFO] MCnebula run: visualize_parent_nebula\n")
    ## get nodes_color data
    metadata = .MCn.class_tree_data
    assign("envir_meta", environment(), envir = parent.env(environment()))
    cat("## visualize_parent_nebula: method_summarize_nebula_index\n")
    class <- pbapply::pblapply(.MCn.ppcp_dataset, method_summarize_nebula_class, 
                               class_data_type = "classes_tree_data",
                               max_number = 1,
                               hierarchy_priority = nodes_color[["hierarchy"]] )
    class <- data.table::rbindlist(class, idcol = T) %>%
      dplyr::select(.id, name) %>%
      dplyr::rename(vis_class = name)
    ## reformat graph, add with class
    graph <- tidygraph::as_tbl_graph(graph)
    ## ---------------------------------------------------------------------- 
    nodes <- graph %>%
      tidygraph::activate(nodes) %>%
      merge(class, by.x = "name" , by.y = ".id", all.x = TRUE, sort = F) %>%
      dplyr::mutate(vis_class = ifelse(is.na(vis_class) == T, "Unknown", vis_class)) %>%
      dplyr::as_tibble()
    edges <- graph %>%
      tidygraph::activate(edges) %>%
      ## rename the col of value of compare spectra
      dplyr::rename(similarity = 3) %>%
      dplyr::as_tibble()
    ## ---------------------------------------------------------------------- 
    graph <- tidygraph::tbl_graph(nodes = nodes, edges = edges)
    ## create network layout
    layout_n <- create_layout(graph, layout = layout, ...)
    ## palette
    palette <- .MCn.palette
    ## draw network via ggraph
    p <- base_vis_p_nebula(layout_n, palette)
    ## write_output
    if(write_output == T){
      ggsave(p, file = paste0(output, "/", "parent_nebula", "/", "parent_nebula.svg"),
             width = width, height = height)
    }
    ## ---------------------------------------------------------------------- 
    rm("envir_meta", envir = parent.env(environment()))
    ## ---------------------------------------------------------------------- 
    cat("[INFO] MCnebula Job Done: visualize_parent_nebula\n")
    if(return_plot == T){
      return(p)
    }
  }
base_vis_p_nebula <-
  function(
           layout_n,
           palette = .MCn.palette,
           ...
           ){
    p <- ggraph(layout_n) + 
      geom_edge_fan(aes(edge_width = similarity),
                    color = "lightblue", show.legend = F) + 
      geom_node_point(aes(size = ifelse(is.na(tanimotoSimilarity) == F,
                                        tanimotoSimilarity, 0.2),
                          fill = stringr::str_wrap(vis_class, width = 25)
                          ),
                      shape = 21
                      ) + 
      scale_fill_manual(values = palette) +
      scale_edge_width(range = c(0.1, 0.7)) + 
      guides(fill = guide_legend(override.aes = list(size = 5))) +
      labs(fill = "Class", size = "Tanimoto similarity") +
      ## ------------------------------------- 
      theme_grey() +
      theme(
            text = element_text(family = "Times"),
            axis.ticks = element_blank(),
            axis.text = element_blank(),
            axis.title = element_blank(),
            panel.background = element_rect(fill = "white"),
            legend.key.width = unit(1, "cm"),
            legend.key.height = unit(1.8, "cm"),
            legend.title = element_text(size = 20, face = "bold"),
            legend.text = element_text(size = 20),
            legend.background = element_rect(fill = "transparent"),
            panel.grid = element_blank(),
            strip.text = element_text(size = 20, face = "bold")
      )
    return(p)
  }