DEGs.R

library(shiny)
library(shinydashboard)
library(stringr)
library(shinyjs)

linebreaks <- function(n){HTML(strrep(br(), n))}


DEGsUI <- function(id, label = "degs"){
  fluidPage(
    shinyjs::useShinyjs(),
    fluidRow(
      br(),
      p("Please select the threshold for the p-value and fold change (FC). The FC threshold will be then transformed to log2 values."),
      p("Only the DEGs which have both the p-value and the FC less than the respective thresholds will be considered in the analyses below."),
      br(),
      h4("Parameter thresholds:"),
      column(4, 
             selectInput(NS(id,"pval"), 
                          p("Adjusted P-value threshold"), 
                          choices = list("NS"=1, "0.05"=0.05, "0.01"=0.01, "0.001"=0.001), 
                          selected = 0.05),
             br(),
             textOutput(NS(id,"selected_pval"))),
      
      column(4, 
             selectInput(NS(id,"FC"), 
                          p("FC threshold"), 
                         choices = list("NS"=1, "1.2"=1.2, "1.5"=1.5, "2"=2), 
                         selected = 1.2),
             br(),
             textOutput(NS(id,"selected_FC"))),
      
      column(4, 
             p("Thresholds Help"),
             helpText("Note: in the options on the left, NS stands for non-significant;",
                      "therefore, the DEGs will not be filtered for either adjusted p-value",
                      "or fold change"))
    ),
    linebreaks(4),
    h4("Download files as ZIP folder?"),
    fluidRow(
      column(3,
             checkboxGroupInput(NS(id, "zips"), "Files to be downloaded as ZIP:",
                                choices = c("Plots"="plots",
                                            "Unfiltered DEGs" = "unfiltered DEGs",
                                            "Filtered DEGs" = "filtered DEGs"))),
      
      column(5, downloadButton(NS(id,'save_zip'), 'Download selected files as a ZIP folder')),
      column(6, 
             helpText("Please note that the few moments may be required to download the files, ",
                      "especially if all three options are chosen"))
    ),
    linebreaks(5),
    h4("Output plots"),
    p("Below you can find the following plots:"),
    tags$ol(
      tags$li("Overview of the sex-biased DEGs - number of DEGs, chromosome fractions of shared DEGs, sex-biased DEGs cellular locations"), 
      tags$li("Presence heatmaps of specific genes of interest - top 20 most frequent sex-specific DEGs, mitochondrial genes and X-escaping genes"), 
      tags$li("Percentage of known cell type markers"),
      tags$li("Presence heatmaps of neuropsychiatric disease markers"), 
      tags$li("Hormone targets enrichment"), 
      tags$li("Percentage of androgen and estrogen response elements (ARE, ERE)"),
      tags$li("Functional Enrichment - gene ontology (biological processes, cellular component, molecular function) and KEGG pathways")
    ),
    linebreaks(2),
    fluidRow(
      tabBox(width = 18,
             height = 1400,
             title = "Overview of sex-biased DEGs",
             id = "Overview_DEGs",
             tabPanel(strong("The number of sex-biased DEGs"),
                      p("Below the number of sex-biased DEGs in each group for each sex and cell type can be found. "),
                      linebreaks(2),
                      imageOutput(NS(id,"num_degs_plot")),
                      linebreaks(45),
                      downloadButton(NS(id,'save_num_degs_plot'), 'Download plot as PNG'),
             ),
             
             tabPanel(strong("Shared DEGs among datasets, colored by chromosome annotation"),
                      p("Below the fractions of which chromosome (Autosome, X or Y) the sex-biased DEGs belong to, ordered by how many groups share the DEGs. The fractions are in logaritmic scale to enhance the lower fractions. "),
                      linebreaks(2),
                      imageOutput(NS(id,"chr_fraction")),
                      linebreaks(45),
                      downloadButton(NS(id,'save_chr_fraction_plot'), 'Download plot as PNG')
             ),
             
             tabPanel(strong('Sex-biased gene locations'),
                      p("In the plot, the frequency of cellular location is indicated by the size, while the color represents the cellular compartment. "),
                      linebreaks(2),
                      imageOutput(NS(id,"GeneLocation")),
                      linebreaks(45),
                      downloadButton(NS(id,'save_GeneLocation_plot'), 'Download plot as PNG')
             )
      )
    ),
    linebreaks(5),
    fluidRow(
      tabBox(width = 18,
             height = 1000,
             title = "Presence heatmaps of specific genes of interest",
             id = "Ind_Hmps",
             tabPanel(strong("Top 20 most differentially present genes"),
                      imageOutput(NS(id,"mostdiffgenes")),
                      linebreaks(20),
                      downloadButton(NS(id,'save_mostdiffgenes_plot'), 'Download plot as PNG')
              ),
             
             tabPanel(strong("Mitochondrial genes"),
                      imageOutput(NS(id,"MTgenes")),
                      linebreaks(20),
                      downloadButton(NS(id,'save_MTgenes_plot'), 'Download plot as PNG')
              ),
             
             tabPanel(strong('X-escaping genes'),
                      imageOutput(NS(id,"Xescapinggenes")),
                      linebreaks(20),
                      downloadButton(NS(id,'save_Xescapinggenes_plot'), 'Download plot as PNG')
              )
      )
    ),
    linebreaks(2),
    box( height = 900, width = 1200,
         strong('Percentage of known cell type markers from McKenzie et al. 2018'),
         imageOutput(NS(id,"McKenzie"))
    ),
    column(3,
           downloadButton(NS(id,'save_McKenzie_plot'), 'Download plot as PNG')
    ),
    linebreaks(2),
    box( height = 900, width = 1200,
         strong("Presence heatmaps of neuropsychiatric disease markers from Chlamydas et al. 2022"),
         imageOutput(NS(id,"Chlamydas"))
    ),
    column(3,
           downloadButton(NS(id,'save_Chlamydas_plot'), 'Download plot as PNG')
    ),
    linebreaks(2),
    box( height = 1300, width = 900,
         strong("Hormone targets enrichment from Jadhav et al. 2022"),
         imageOutput(NS(id,"Hormones"))
    ),
    column(3,
           downloadButton(NS(id,'save_Hormones_plot'), 'Download plot as PNG')
    ),
    linebreaks(2),
    fluidRow(
      column(6,
             box( height = 900, width = 500,
                  strong('Percentages of ARE sites among the sex-biased DEGs'),
                  imageOutput(NS(id,"ARE"))),
             downloadButton(NS(id,'save_ARE_plot'), 'Download plot as PNG')),
      column(6,
             box( height = 900, width = 500,
                  strong('Percentages of ERE sites among the sex-biased DEGs'),
                  imageOutput(NS(id,"ERE"))),
             downloadButton(NS(id,'save_ERE_plot'), 'Download plot as PNG'))
    ),
    linebreaks(5),
    fluidRow(
      tabBox(width = 18,
             height = 2000,
             title = "Functional Enrichment",
             id = "Functional_enrichment",
             tabPanel(strong("Gene Ontology (GO) - Biological Processes"),
                      imageOutput(NS(id,"GOBP")),
                      linebreaks(70),
                      downloadButton(NS(id,'save_GOBP_plot'), 'Download plot as PNG')
             ),
             
             tabPanel(strong("Gene Ontology (GO) - Cellular Components"),
                      imageOutput(NS(id,"GOCC")),
                      linebreaks(70),
                      downloadButton(NS(id,'save_GOCC_plot'), 'Download plot as PNG')
             ),
             
             tabPanel(strong("Gene Ontology (GO) - Molecular Functions"),
                      imageOutput(NS(id,"GOMF")),
                      linebreaks(70),
                      downloadButton(NS(id,'save_GOMF_plot'), 'Download plot as PNG')
             ),
             
             tabPanel(strong("Kyoto Encyclopedia of Genes and Genomes (KEGG) - pathway enrichment"),
                      imageOutput(NS(id,"KEGG")),
                      linebreaks(70),
                      downloadButton(NS(id,'save_KEGG_plot'), 'Download plot as PNG')
             )
      )
    ),
  )
}

DEGsServer <- function(id) {
  
  moduleServer(id, function(input, output, session) {
  
    output$selected_pval <- renderText({ 
      paste0("You have selected this adjusted p-value threshold: ", input$pval)
    })
    
    output$selected_FC <- renderText({ 
      paste0("You have selected this FC threshold: ", input$FC)
    })
    
    observe({
      shinyjs::toggleState("save_zip", condition = !is.null(input$zips))
    })
 
    output$save_zip <- downloadHandler(
      filename = paste0("HumanBrainSexSingleCell_download.zip"),
      contentType = "application/zip",
      content = function(file){
        
        plt_dir <- paste0("www/Plots/pval_", str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","))
        plt_files <- list.dirs(plt_dir, full.names = T, recursive = T)
        
        unfilt_DEGs_dir <- "data/Unfiltered_DEGs"
        unfilt_files <- list.dirs(unfilt_DEGs_dir, full.names = T, recursive = T)
        
        filt_DEGs_dir <- paste0("data/Filtered_DEGs/pval_", str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","))
        filt_files <- list.dirs(filt_DEGs_dir, full.names = T, recursive = T)
        
        files_ls <- list("plots"=plt_files,
                         "unfiltered DEGs"=unfilt_files,
                         "filtered DEGs"=filt_files)
        
        files <- unlist(files_ls[names(files_ls) %in% input$zips], use.names = F)

        #create the zip file
        zip(file, files)
        
      }
    )
    
    output$num_degs_plot <- renderImage({
      filename <- normalizePath(file.path(paste0("www/Plots/pval_", 
                                str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), 
                                "/Number_of_DEGs.png")))
      list(src = filename, height = 1200, width = 750)
    }, deleteFile = FALSE)
    
    
    output$save_num_degs_plot <- downloadHandler(
      filename = paste0("Number_of_DEGs_pval_", str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), ".png"),
      content = function(file) {
        file.copy(normalizePath(file.path(paste0("www/Plots/pval_", 
                                                 str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), 
                                                 "/Number_of_DEGs.png"))), file)
      }
    )
    
    output$chr_fraction <- renderImage({
      filename <- normalizePath(file.path(paste0("www/Plots/pval_", 
                                                 str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), 
                                                 "/Chr_fractions.png")))
      list(src = filename, height = 1200, width = 750)
    }, deleteFile = FALSE)
    
    output$save_chr_fraction_plot <- downloadHandler(
      filename = paste0("Chr_fraction_pval_", str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), ".png"),
      contentType = "image/png",
      content = function(file) {
        file.copy(normalizePath(file.path(paste0("www/Plots/pval_", 
                                                 str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), 
                                                 "/Chr_fractions.png"))), file)
      }
    )  
    
    output$GeneLocation <- renderImage({
      filename <- normalizePath(file.path(paste0("www/Plots/pval_", 
                                                 str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), 
                                                 "/Location.png")))
      list(src = filename, height = 1200, width = 900)
    }, deleteFile = FALSE)
    
    output$save_GeneLocation_plot <- downloadHandler(
      filename = paste0("Location_pval_", str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), ".png"),
      contentType = "image/png",
      content = function(file) {
        file.copy(normalizePath(file.path(paste0("www/Plots/pval_", 
                                                 str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), 
                                                 "/Location.png"))), file)
      }
    )  
    
    output$mostdiffgenes <- renderImage({
      filename <- normalizePath(file.path(paste0("www/Plots/pval_", 
                                                 str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), 
                                                 "/top_20_most_diff_genes.png")))
      list(src = filename, height = 800, width = 1400)
    }, deleteFile = FALSE)
    
    output$save_mostdiffgenes_plot <- downloadHandler(
      filename = paste0("Top_20_most_diff_genes_pval_", str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), ".png"),
      contentType = "image/png",
      content = function(file) {
        file.copy(normalizePath(file.path(paste0("www/Plots/pval_", 
                                                 str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), 
                                                 "/top_20_most_diff_genes.png"))), file)
      }
    )  
    
    output$MTgenes <- renderImage({
      filename <- normalizePath(file.path(paste0("www/Plots/pval_", 
                                                 str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), 
                                                 "/MT_genes.png")))
      list(src = filename, height = 800, width = 1400)
    }, deleteFile = FALSE)
    
    output$save_MTgenes_plot <- downloadHandler(
      filename = paste0("MT_genes_pval_", str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), ".png"),
      contentType = "image/png",
      content = function(file) {
        file.copy(normalizePath(file.path(paste0("www/Plots/pval_", 
                                                 str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), 
                                                 "/MT_genes.png"))), file)
      }
    )  
    
    output$Xescapinggenes <- renderImage({
      filename <- normalizePath(file.path(paste0("www/Plots/pval_", 
                                                 str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), 
                                                 "/X_escaping_genes.png")))
      list(src = filename, height = 800, width = 1400)
    }, deleteFile = FALSE)
    
    output$save_Xescapinggenes_plot <- downloadHandler(
      filename = paste0("X_escaping_genes_pval_", str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), ".png"),
      contentType = "image/png",
      content = function(file) {
        file.copy(normalizePath(file.path(paste0("www/Plots/pval_", 
                                                 str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), 
                                                 "/X_escaping_genes.png"))), file)
      }
    )  
    
    
    output$McKenzie <- renderImage({
      filename <- normalizePath(file.path(paste0("www/Plots/pval_", 
                                                 str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), 
                                                 "/McKenzie_perc.png")))
      list(src = filename, height = 800, width = 1400)
    }, deleteFile = FALSE)
    
    output$save_McKenzie_plot <- downloadHandler(
      filename = paste0("McKenzie_percentages_pval_", str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), ".png"),
      contentType = "image/png",
      content = function(file) {
        file.copy(normalizePath(file.path(paste0("www/Plots/pval_", 
                                                 str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), 
                                                 "/McKenzie_perc.png"))), file)
      }
    )  
    
    output$Chlamydas <- renderImage({
      filename <- normalizePath(file.path(paste0("www/Plots/pval_", 
                                                 str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), 
                                                 "/Chlamydas_hmp.png")))
      list(src = filename, height = 800, width = 1400)
    }, deleteFile = FALSE)
    
    output$save_Chlamydas_plot <- downloadHandler(
      filename = paste0("Chlamydas_hmp_pval_", str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), ".png"),
      contentType = "image/png",
      content = function(file) {
        file.copy(normalizePath(file.path(paste0("www/Plots/pval_", 
                                                 str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), 
                                                 "/Chlamydas_hmp.png"))), file)
      }
    )  
    
    output$Hormones <- renderImage({
      filename <- normalizePath(file.path(paste0("www/Plots/pval_", 
                                                 str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), 
                                                 "/Hormone_target_enrichment.png")))
      list(src = filename, height = 1200, width = 800)
    }, deleteFile = FALSE)
    
    output$save_Hormones_plot <- downloadHandler(
      filename = paste0("Hormone_target_enrichment_pval_", str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), ".png"),
      contentType = "image/png",
      content = function(file) {
        file.copy(normalizePath(file.path(paste0("www/Plots/pval_", 
                                                 str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), 
                                                 "/Hormone_target_enrichment.png"))), file)
      }
    )  
    
    output$ARE <- renderImage({
      filename <- normalizePath(file.path(paste0("www/Plots/pval_", 
                                                 str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), 
                                                 "/ARE.png")))
      list(src = filename, height = 800, width = 700)
    }, deleteFile = FALSE)
    
    output$save_ARE_plot <- downloadHandler(
      filename = paste0("ARE_sites_pval_", str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), ".png"),
      contentType = "image/png",
      content = function(file) {
        file.copy(normalizePath(file.path(paste0("www/Plots/pval_", 
                                                 str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), 
                                                 "/ARE.png"))), file)
      }
    )  
    
    output$ERE <- renderImage({
      filename <- normalizePath(file.path(paste0("www/Plots/pval_", 
                                                 str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), 
                                                 "/ERE.png")))
      list(src = filename, height = 800, width = 700)
    }, deleteFile = FALSE)
    
    output$save_ERE_plot <- downloadHandler(
      filename = paste0("ERE_sites_pval_", str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), ".png"),
      contentType = "image/png",
      content = function(file) {
        file.copy(normalizePath(file.path(paste0("www/Plots/pval_", 
                                                 str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), 
                                                 "/ERE.png"))), file)
      }
    )  
    
    output$GOBP <- renderImage({
      filename <- normalizePath(file.path(paste0("www/Plots/pval_", 
                                                 str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), 
                                                 "/GO_BP.png")))
      list(src = filename, height = 1600, width = 1400)
    }, deleteFile = FALSE)
    
    output$save_GOBP_plot <- downloadHandler(
      filename = paste0("GO_BP_sites_pval_", str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), ".png"),
      contentType = "image/png",
      content = function(file) {
        file.copy(normalizePath(file.path(paste0("www/Plots/pval_", 
                                                 str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), 
                                                 "/GO_BP.png"))), file)
      }
    )  
    
    output$GOCC <- renderImage({
      filename <- normalizePath(file.path(paste0("www/Plots/pval_", 
                                                 str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), 
                                                 "/GO_CC.png")))
      list(src = filename, height = 1600, width = 1400)
    }, deleteFile = FALSE)
    
    output$save_GOCC_plot <- downloadHandler(
      filename = paste0("GO_CC_sites_pval_", str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), ".png"),
      contentType = "image/png",
      content = function(file) {
        file.copy(normalizePath(file.path(paste0("www/Plots/pval_", 
                                                 str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), 
                                                 "/GO_CC.png"))), file)
      }
    )  
    
    output$GOMF <- renderImage({
      filename <- normalizePath(file.path(paste0("www/Plots/pval_", 
                                                 str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), 
                                                 "/GO_MF.png")))
      list(src = filename, height = 1600, width = 1400)
    }, deleteFile = FALSE)
    
    output$save_GOMF_plot <- downloadHandler(
      filename = paste0("GO_MF_sites_pval_", str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), ".png"),
      contentType = "image/png",
      content = function(file) {
        file.copy(normalizePath(file.path(paste0("www/Plots/pval_", 
                                                 str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), 
                                                 "/GO_MF.png"))), file)
      }
    )  
    
    output$KEGG <- renderImage({
      filename <- normalizePath(file.path(paste0("www/Plots/pval_", 
                                                 str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), 
                                                 "/KEGG.png")))
      list(src = filename, height = 1600, width = 1400)
    }, deleteFile = FALSE)
    
    output$save_KEGG_plot <- downloadHandler(
      filename = paste0("KEGG_sites_pval_", str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), ".png"),
      contentType = "image/png",
      content = function(file) {
        file.copy(normalizePath(file.path(paste0("www/Plots/pval_", 
                                                 str_replace(input$pval, "\\.",  ","), "_FC_", str_replace(input$FC, "\\.",  ","), 
                                                 "/KEGG.png"))), file)
      }
    )  
    
  
  })
  
}