R/mod_cnet_plot.R

In igemsoftwareadmin/ClusteRsy-Linkoping: ClusteRsy

#' cnet_plot UI Function
#'
#' @description A shiny Module.
#'
#' @param id,input,output,session Internal parameters for {shiny}.
#'
#' @noRd 
#'
#' @importFrom shiny NS tagList 
mod_cnet_plot_ui <- function(id){
  ns <- NS(id)
  tagList(
          plotOutput(ns("cnet_plot"), height = '100vh', width = '100%') %>% shinycssloaders::withSpinner(color="#ffbd40", 
                                                                                                         type = 4,
                                                                                                         size = 0.8)
  )
}
    
#' cnet_plot Server Function
#'
#' @noRd 
mod_cnet_plot_server <- function(input, output, session, cnet_plot_para_ui_1, selected, con){
  ns <- session$ns
  
  cnetplot <- reactive({
    enrichment_objects <- MODifieRDB::get_available_enrichment_objects(con)
    enrichment_object <- MODifieRDB::enrichment_object_from_db(enrichment_objects$enrichment_name[selected$selected_object], con)
    enrichment_object_readable <- DOSE::setReadable(enrichment_object, OrgDb = 'org.Hs.eg.db', keyType = "ENTREZID") #Not sure if KeyType should be selected from the enrichment object
    
    input_name <- MODifieRDB::get_input_name_by_enrichment_row(enrichment_objects$enrichment_name[selected$selected_object], con)
    edgeR_deg_table <- MODifieRDB::MODifieR_input_from_db(input_name, con)$edgeR_deg_table
    logFC <- edgeR_deg_table$logFC %>% set_names(. , rownames(edgeR_deg_table))

    p <- try(enrichplot::cnetplot(x = enrichment_object_readable,
                              showCategory = cnet_plot_para_ui_1$showcategory,
                              foldChange = logFC,
                              layout = cnet_plot_para_ui_1$layout,
                              circular = cnet_plot_para_ui_1$circular,
                              colorEdge = cnet_plot_para_ui_1$colorEdge,
                              node_label = cnet_plot_para_ui_1$node_label,
                              ) + ggplot2::ggtitle(label = cnet_plot_para_ui_1$title))
    
    return(p)
  })
  
  output$cnet_plot <- renderPlot({
    cnetplot() #calling the reactive plot
  })
}
    
## To be copied in the UI
# mod_cnet_plot_ui("cnet_plot_ui_1")
    
## To be copied in the server
# callModule(mod_cnet_plot_server, "cnet_plot_ui_1")