added tab summary info

Breeding-Insight · Sep 24, 2024 · 86bbcbf · 86bbcbf
1 parent cc49743
commit 86bbcbf
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Showing 10 changed files with 536 additions and 18 deletions.
diff --git a/R/app_ui.R b/R/app_ui.R
@@ -44,18 +44,18 @@ app_ui <- function(request) {
         sidebarMenu(id = "MainMenu",
           flat = FALSE,
           tags$li(class = "header", style = "color: grey; margin-top: 10px; margin-bottom: 10px; padding-left: 15px;", "Menu"),
-          menuItem("Home", tabName = "welcome", icon = icon("house")),
+                   menuItem("Home", tabName = "welcome", icon = icon("house")),
           tags$li(class = "header", style = "color: grey; margin-top: 18px; margin-bottom: 10px; padding-left: 15px;", "Genotype Processing"),
                    menuItem("DArT Report2VCF", tabName = "dosage2vcf", icon = icon("share-from-square")),
                    menuItem("Updog Dosage Calling", tabName = "updog", icon = icon("list-ol")),
                    menuItem("VCF Filtering", tabName = "filtering", icon = icon("filter")),
+          tags$li(class = "header", style = "color: grey; margin-top: 18px; margin-bottom: 10px; padding-left: 15px;", "Summary Metrics"),
+                   menuItem("Genomic Diversity", tabName = "diversity", icon = icon("chart-pie")),
           tags$li(class = "header", style = "color: grey; margin-top: 18px; margin-bottom: 10px; padding-left: 15px;", "Population Structure"),
                    menuItem("PCA", tabName = "pca", icon = icon("chart-simple")),
                    menuItem("DAPC", tabName = "dapc", icon = icon("circle-nodes")),
-          tags$li(class = "header", style = "color: grey; margin-top: 18px; margin-bottom: 10px; padding-left: 15px;", "Summary Metrics"),
-          menuItem("Genomic Diversity", tabName = "diversity", icon = icon("chart-pie")),
           tags$li(class = "header", style = "color: grey; margin-top: 18px; margin-bottom: 10px; padding-left: 15px;", "GWAS"),
-          menuItem("GWASpoly", tabName = "gwas", icon = icon("think-peaks")),
+                   menuItem("GWASpoly", tabName = "gwas", icon = icon("think-peaks")),
           tags$li(class = "header", style = "color: grey; margin-top: 18px; margin-bottom: 10px; padding-left: 15px;", "Genomic Selection"),
                   menuItem(
                     span("Predictive Ability", bs4Badge("beta", position = "right", color = "success")),

diff --git a/R/mod_DosageCall.R b/R/mod_DosageCall.R
@@ -88,7 +88,8 @@ mod_DosageCall_ui <- function(id){
             p(HTML("<b>Parameters description:</b>"), actionButton(ns("goPar"), icon("arrow-up-right-from-square", verify_fa = FALSE) )), hr(),
             p(HTML("<b>Results description:</b>"), actionButton(ns("goRes"), icon("arrow-up-right-from-square", verify_fa = FALSE) )), hr(),
             p(HTML("<b>How to cite:</b>"), actionButton(ns("goCite"), icon("arrow-up-right-from-square", verify_fa = FALSE) )), hr(),
-            p(HTML("<b>Updog tutorial:</b>"), actionButton(ns("goUpdog"), icon("arrow-up-right-from-square", verify_fa = FALSE), onclick ="window.open('https://dcgerard.github.io/updog/', '_blank')" )),
+            p(HTML("<b>Updog tutorial:</b>"), actionButton(ns("goUpdog"), icon("arrow-up-right-from-square", verify_fa = FALSE), onclick ="window.open('https://dcgerard.github.io/updog/', '_blank')" )), hr(),
+            actionButton(ns("dosage_summary"), "Summary"),
             circle = FALSE,
             status = "warning",
             icon = icon("info"), width = "500px",
@@ -429,6 +430,68 @@ mod_DosageCall_server <- function(input, output, session, parent_session){
       ex <- system.file("iris_DArT_MADC.csv", package = "BIGapp")
       file.copy(ex, file)
     })
+
+  ##Summary Info
+  dosage_summary_info <- function() {
+    #Handle possible NULL values for inputs
+    genotype_file_name <- if (!is.null(input$madc_file$name)) input$madc_file$name else "No file selected"
+    report_file_name <- if (!is.null(input$madc_passport$name)) input$madc_passport$name else "No file selected"
+    selected_ploidy <- if (!is.null(input$ploidy)) as.character(input$ploidy) else "Not selected"
+
+    #Print the summary information
+    cat(
+      "BIGapp Dosage Calling Summary\n",
+      "\n",
+      paste0("Date: ", Sys.Date()), "\n",
+      paste("R Version:", R.Version()$version.string), "\n",
+      "\n",
+      "### Input Files ###\n",
+      "\n",
+      paste("Input Genotype File:", genotype_file_name), "\n",
+      paste("Input Passport File:", report_file_name), "\n",
+      "\n",
+      "### User Selected Parameters ###\n",
+      "\n",
+      paste("Selected Ploidy:", selected_ploidy), "\n",
+      paste("Selected Updog Model:", input$updog_model), "\n",
+      "\n",
+      "### R Packages Used ###\n",
+      "\n",
+      paste("BIGapp:", packageVersion("BIGapp")), "\n",
+      paste("BIGr:", packageVersion("BIGr")), "\n",
+      paste("Updog:", packageVersion("updog")), "\n",
+      paste("dplyr:", packageVersion("dplyr")), "\n",
+      sep = ""
+    )
+  }
+
+  # Popup for analysis summary
+  observeEvent(input$dosage_summary, {
+    showModal(modalDialog(
+      title = "Summary Information",
+      size = "l",
+      easyClose = TRUE,
+      footer = tagList(
+        modalButton("Close"),
+        downloadButton("download_dosage_info", "Download")
+      ),
+      pre(
+        paste(capture.output(dosage_summary_info()), collapse = "\n")
+      )
+    ))
+  })
+
+
+  # Download Summary Info
+  output$download_dosage_info <- downloadHandler(
+    filename = function() {
+      paste("DosageCalling_summary_", Sys.Date(), ".txt", sep = "")
+    },
+    content = function(file) {
+      # Write the summary info to a file
+      writeLines(paste(capture.output(dosage_summary_info()), collapse = "\n"), file)
+    }
+  )
 }
 
 ## To be copied in the UI

diff --git a/R/mod_Filtering.R b/R/mod_Filtering.R
@@ -46,10 +46,8 @@ mod_Filtering_ui <- function(id){
                  div(style="display:inline-block; float:right",dropdownButton(
                    tags$h3("Updog Filter Parameters"),
                    "You can download examples of the expected file here: \n",
-                   downloadButton(ns('download_vcf'), "Download VCF Example File"),
-                   # "Add description of each filter. Presently, all filtering parameters that are typically used for processing
-                   #  a VCF file from Updog dosage calling are included. If a VCF file does not contain these values, it will only be
-                   #  filtered for read depth, missing data, and maf.",
+                   downloadButton(ns('download_vcf'), "Download VCF Example File"), hr(),
+                   actionButton(ns("filtering_summary"), "Summary"),
                    circle = FALSE,
                    status = "warning",
                    icon = icon("info"), width = "300px",
@@ -624,6 +622,74 @@ mod_Filtering_server <- function(input, output, session, parent_session){
       ex <- system.file("iris_DArT_VCF.vcf.gz", package = "BIGapp")
       file.copy(ex, file)
     })
+
+  ##Summary Info
+  filtering_summary_info <- function() {
+    #Handle possible NULL values for inputs
+    genotype_file_name <- if (!is.null(input$updog_rdata$name)) input$updog_rdata$name else "No file selected"
+    selected_ploidy <- if (!is.null(input$filter_ploidy)) as.character(input$filter_ploidy) else "Not selected"
+
+    #Print the summary information
+    cat(
+      "BIGapp VCF Filtering Summary\n",
+      "\n",
+      paste0("Date: ", Sys.Date()), "\n",
+      paste(R.Version()$version.string), "\n",
+      "\n",
+      "### Input Files ###\n",
+      "\n",
+      paste("Input Genotype File:", genotype_file_name), "\n",
+      "\n",
+      "### User Selected Parameters ###\n",
+      "\n",
+      paste("Selected Ploidy:", selected_ploidy), "\n",
+      paste("MAF Filter:", input$filter_maf), "\n",
+      paste("Min Read Depth (Marker per Sample):", input$size_depth), "\n",
+      paste("Remove SNPs with >= % missing data:", input$snp_miss), "\n",
+      paste("Remove Samples with >= % missing data:", input$sample_miss), "\n",
+      paste("Use Updog Filtering Parameters?:", input$use_updog), "\n",
+      paste("Max OD (Updog filter):", ifelse(input$use_updog,input$OD_filter, "NA")), "\n",
+      paste("Bias Minimum (Updog filter):", ifelse(input$use_updog,input$Bias[1], "NA")), "\n",
+      paste("Bias Maximum (Updog filter):", ifelse(input$use_updog,input$Bias[2], "NA")), "\n",
+      paste("Max Prop_mis (Updog filter):", ifelse(input$use_updog,input$Prop_mis,"NA")), "\n",
+      paste("Minimum maxpostprob (Updog filter):", ifelse(input$use_updog,input$maxpostprob_filter,"NA")), "\n",
+      "\n",
+      "### R Packages Used ###\n",
+      "\n",
+      paste("BIGapp:", packageVersion("BIGapp")), "\n",
+      paste("BIGr:", packageVersion("BIGr")), "\n",
+      paste("Updog:", packageVersion("updog")), "\n",
+      sep = ""
+    )
+  }
+
+  # Popup for analysis summary
+  observeEvent(input$filtering_summary, {
+    showModal(modalDialog(
+      title = "Summary Information",
+      size = "l",
+      easyClose = TRUE,
+      footer = tagList(
+        modalButton("Close"),
+        downloadButton("download_filtering_info", "Download")
+      ),
+      pre(
+        paste(capture.output(filtering_summary_info()), collapse = "\n")
+      )
+    ))
+  })
+
+
+  # Download Summary Info
+  output$download_filtering_info <- downloadHandler(
+    filename = function() {
+      paste("Filtering_summary_", Sys.Date(), ".txt", sep = "")
+    },
+    content = function(file) {
+      # Write the summary info to a file
+      writeLines(paste(capture.output(filtering_summary_info()), collapse = "\n"), file)
+    }
+  )
 }
 
 ## To be copied in the UI

diff --git a/R/mod_GS.R b/R/mod_GS.R
@@ -46,9 +46,8 @@ mod_GS_ui <- function(id){
                    "You can download examples of the expected input input files here: \n",
                    downloadButton(ns('download_vcft'), "Download Training VCF Example File"),
                    downloadButton(ns('download_pheno'), "Download Passport Example File"),
-                   downloadButton(ns('download_vcfp'), "Download Prediction VCF Example File"),
-
-                   #"GP uses the rrBLUP package: It can impute missing data, adapt to different ploidy, perform 5-fold cross validations with different number of iterations, run multiple traits, and accept multiple fixed effects.",
+                   downloadButton(ns('download_vcfp'), "Download Prediction VCF Example File"),hr(),
+                   actionButton(ns("pred_summary"), "Summary"),
                    circle = FALSE,
                    status = "warning",
                    icon = icon("info"), width = "300px",
@@ -720,6 +719,76 @@ mod_GS_server <- function(input, output, session, parent_session){
       ex <- system.file("iris_passport_file.csv", package = "BIGapp")
       file.copy(ex, file)
     })
+
+  ##Summary Info
+  pred_summary_info <- function() {
+    # Handle possible NULL values for inputs
+    dosage_file_name <- if (!is.null(input$pred_known_file$name)) input$pred_known_file$name else "No file selected"
+    est_file_name <- if (!is.null(input$pred_est_file$name)) input$pred_est_file$name else "No file selected"
+    passport_file_name <- if (!is.null(input$pred_trait_file$name)) input$pred_trait_file$name else "No file selected"
+    selected_ploidy <- if (!is.null(input$pred_est_ploidy)) as.character(input$pred_est_ploidy) else "Not selected"
+
+    # Print the summary information
+    cat(
+      "BIGapp Selection Summary\n",
+      "\n",
+      paste0("Date: ", Sys.Date()), "\n",
+      paste("R Version:", R.Version()$version.string), "\n",
+      "\n",
+      "### Input Files ###\n",
+      "\n",
+      paste("Input Genotype File 1:", dosage_file_name), "\n",
+      paste("Input Genotype File 2:", est_file_name), "\n",
+      paste("Input Passport File:", passport_file_name), "\n",
+      "\n",
+      "### User Selected Parameters ###\n",
+      "\n",
+      paste("Selected Ploidy:", selected_ploidy), "\n",
+      paste("Selected Trait(s):", input$pred_trait_info2), "\n",
+      paste("Selected Fixed Effects:", input$pred_fixed_info2), "\n",
+      #paste("Selected Model:", input$pred_fixed_info2), "\n",
+      #paste("Selected Matrix:", input$pred_fixed_info2), "\n",
+      "\n",
+      "### R Packages Used ###\n",
+      "\n",
+      paste("BIGapp:", packageVersion("BIGapp")), "\n",
+      paste("AGHmatrix:", packageVersion("AGHmatrix")), "\n",
+      paste("ggplot2:", packageVersion("ggplot2")), "\n",
+      paste("rrBLUP:", packageVersion("rrBLUP")), "\n",
+      paste("vcfR:", packageVersion("vcfR")), "\n",
+      paste("dplyr:", packageVersion("dplyr")), "\n",
+      paste("tidyr:", packageVersion("tidyr")), "\n",
+      sep = ""
+    )
+  }
+
+  # Popup for analysis summary
+  observeEvent(input$pred_summary, {
+    showModal(modalDialog(
+      title = "Summary Information",
+      size = "l",
+      easyClose = TRUE,
+      footer = tagList(
+        modalButton("Close"),
+        downloadButton("download_pred_info", "Download")
+      ),
+      pre(
+        paste(capture.output(pred_summary_info()), collapse = "\n")
+      )
+    ))
+  })
+
+
+  # Download Summary Info
+  output$download_pred_info <- downloadHandler(
+    filename = function() {
+      paste("pred_summary_", Sys.Date(), ".txt", sep = "")
+    },
+    content = function(file) {
+      # Write the summary info to a file
+      writeLines(paste(capture.output(pred_summary_info()), collapse = "\n"), file)
+    }
+  )
 }
 
 ## To be copied in the UI

diff --git a/R/mod_GSAcc.R b/R/mod_GSAcc.R
@@ -58,7 +58,8 @@ mod_GSAcc_ui <- function(id){
                    tags$h3("GP Parameters"),
                    "You can download examples of the expected input input files here: \n",
                    downloadButton(ns('download_vcf'), "Download VCF Example File"),
-                   downloadButton(ns('download_pheno'), "Download Passport Example File"),
+                   downloadButton(ns('download_pheno'), "Download Passport Example File"),hr(),
+                   actionButton(ns("predAcc_summary"), "Summary"),
                    circle = FALSE,
                    status = "warning",
                    icon = icon("info"), width = "300px",
@@ -783,6 +784,74 @@ mod_GSAcc_server <- function(input, output, session, parent_session){
       ex <- system.file("iris_passport_file.csv", package = "BIGapp")
       file.copy(ex, file)
     })
+
+  ##Summary Info
+  predAcc_summary_info <- function() {
+    # Handle possible NULL values for inputs
+    dosage_file_name <- if (!is.null(input$pred_file$name)) input$pred_file$name else "No file selected"
+    passport_file_name <- if (!is.null(input$trait_file$name)) input$trait_file$name else "No file selected"
+    selected_ploidy <- if (!is.null(input$pred_ploidy)) as.character(input$pred_ploidy) else "Not selected"
+
+    # Print the summary information
+    cat(
+      "BIGapp Selection Model CV Summary\n",
+      "\n",
+      paste0("Date: ", Sys.Date()), "\n",
+      paste("R Version:", R.Version()$version.string), "\n",
+      "\n",
+      "### Input Files ###\n",
+      "\n",
+      paste("Input Genotype File:", dosage_file_name), "\n",
+      paste("Input Passport File:", passport_file_name), "\n",
+      "\n",
+      "### User Selected Parameters ###\n",
+      "\n",
+      paste("Selected Ploidy:", selected_ploidy), "\n",
+      paste("Selected Trait(s):", input$pred_trait_info), "\n",
+      paste("Selected Fixed Effects:", input$pred_fixed_info), "\n",
+      paste("Selected Model:", advanced_options$pred_model), "\n",
+      paste("Selected Matrix:", advanced_options$pred_matrix), "\n",
+      "\n",
+      "### R Packages Used ###\n",
+      "\n",
+      paste("BIGapp:", packageVersion("BIGapp")), "\n",
+      paste("AGHmatrix:", packageVersion("AGHmatrix")), "\n",
+      paste("ggplot2:", packageVersion("ggplot2")), "\n",
+      paste("rrBLUP:", packageVersion("rrBLUP")), "\n",
+      paste("vcfR:", packageVersion("vcfR")), "\n",
+      paste("dplyr:", packageVersion("dplyr")), "\n",
+      paste("tidyr:", packageVersion("tidyr")), "\n",
+      sep = ""
+    )
+  }
+
+  # Popup for analysis summary
+  observeEvent(input$predAcc_summary, {
+    showModal(modalDialog(
+      title = "Summary Information",
+      size = "l",
+      easyClose = TRUE,
+      footer = tagList(
+        modalButton("Close"),
+        downloadButton("download_predAcc_info", "Download")
+      ),
+      pre(
+        paste(capture.output(predAcc_summary_info()), collapse = "\n")
+      )
+    ))
+  })
+
+
+  # Download Summary Info
+  output$download_predAcc_info <- downloadHandler(
+    filename = function() {
+      paste("predAcc_summary_", Sys.Date(), ".txt", sep = "")
+    },
+    content = function(file) {
+      # Write the summary info to a file
+      writeLines(paste(capture.output(predAcc_summary_info()), collapse = "\n"), file)
+    }
+  )
 }
 
 ## To be copied in the UI

diff --git a/R/mod_PCA.R b/R/mod_PCA.R
@@ -35,7 +35,7 @@ mod_PCA_ui <- function(id){
                      tags$h3("PCA Inputs"),
                      "You can download examples of the expected files here: \n",
                      downloadButton(ns('download_vcf'), "Download VCF Example File"),
-                     downloadButton(ns('download_pheno'), "Download Passport Example File"),
+                     downloadButton(ns('download_pheno'), "Download Passport Example File"),hr(),
                      actionButton(ns("pca_summary"), "Summary"),
                      circle = FALSE,
                      status = "warning",