R/ggnetwork_plot_full.R

In neurogenomics/MultiEWCE: Multi-Scale Target Explorer

#' Create interactive network plot start to finish
#'
#' This puts all the functions together from getting the subset of results
#'  to creating the final interactive plot.
#'
#' @param results The cell type-phenotype enrichment results generated by
#'  \link[MSTExplorer]{gen_results}
#'  and merged together with \link[MSTExplorer]{merge_results}
#' @param q_threshold The q value threshold to subset the \code{results} by.
#' @param effect_threshold The minimum fold change in specific expression
#'  to subset the \code{results} by.
#' @inheritParams HPOExplorer::make_phenos_dataframe
#' @inheritParams HPOExplorer::make_network_plot
#' @inheritParams HPOExplorer::filter_descendants
#' @inheritParams HPOExplorer::make_network_object
#' @inheritParams KGExplorer::filter_dt
#' @inheritDotParams HPOExplorer::make_network_plot
#' @returns A named list of outputs,
#'  including a interactive network plot of the selected subset
#' of results from RD EWCE analysis.
#'
#' @export
#' @import HPOExplorer
#' @import KGExplorer
#' @examples
#' res <- ggnetwork_plot_full(filters = list(CellType = "Microglia"))
ggnetwork_plot_full <- function(filters,
                                keep_descendants = NULL,
                                results = load_example_results(),
                                hpo = HPOExplorer::get_hpo(),
                                q_threshold = 0.0005,
                                effect_threshold = 1,
                                columns = HPOExplorer::list_columns(),
                                colour_var = "effect",
                                size_var = "ontLvl_relative",
                                add_ont_lvl_absolute = TRUE,
                                add_ont_lvl_relative = TRUE,
                                method = c("ggnetwork","visnetwork"),
                                interactive = TRUE,
                                verbose = TRUE,
                                ...){
  messager("ggnetwork_plot_full",v=verbose)
  phenos <- subset_phenos(filters = filters,
                          keep_descendants = keep_descendants,
                          results = results,
                          hpo = hpo,
                          q_threshold = q_threshold,
                          effect_threshold = effect_threshold,
                          verbose = verbose)
  phenos <- HPOExplorer::add_hpo_name(phenos = phenos,
                                      hpo = hpo)
  #### Aggregate across multiple celltypes ####
  phenos <- agg_results(phenos = phenos,
                        count_var = "CellType",
                        group_var = c("hpo_name","hpo_id"),
                        verbose = verbose)
  #### Add metadata ####
  if(isTRUE(add_ont_lvl_absolute)){
    phenos <- HPOExplorer::add_ont_lvl(phenos = phenos,
                                       hpo = hpo,
                                       absolute = TRUE)
  }
  if(isTRUE(add_ont_lvl_relative)){
    phenos <- HPOExplorer::add_ont_lvl(phenos = phenos,
                                       hpo = hpo,
                                       absolute = FALSE)
  }
  phenos <- HPOExplorer::add_hpo_definition(phenos = phenos,
                                            verbose = verbose)
  phenos <- KGExplorer::add_hoverboxes(g = phenos,
                                       columns = names(columns),
                                       hoverbox_column = "hover",
                                       as_html = interactive)
  #### Fix colour var for aggregated data ####
  colour_var2 <- paste0("mean_",colour_var)
  if(!colour_var %in% names(phenos) &&
     colour_var2 %in% names(phenos)){
    colour_var <- colour_var2
  }
  #### Make plot ####
  out <- HPOExplorer::make_network_plot(phenos = phenos,
                                        colour_var = colour_var,
                                        size_var = size_var,
                                        interactive = interactive,
                                        method = method,
                                        ...)
  #### Return ####
  return(out)
}