UI and Logo Updates

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: BIGapp
 Title: Breeding Insight Genomics Shiny Application
-Version: 0.6.2
+Version: 1.0.0
 Authors@R: 
     c(
               person(c("Alexander", "M."), "Sandercock",
@@ -20,10 +20,9 @@ Authors@R:
                     role = "aut"),
               person("Breeding Insight Team",
                     role = "aut"))
-Description: This R shiny app provides a web-based user friendly way for our internal and 
-             external collaborators to analyze genomic data without needing to use command-line tools.
+Description: This R shiny app provides a web-based user friendly way for researchers to analyze genomic data without needing to use command-line tools.
              Initial supported analyses will include the mature genomics/bioinformatics pipelines developed 
-             within Breeding Insight, with additional analyses continuing to be added.
+             within Breeding Insight, with additional analyses continuing to be added. Both diploid and polyploid species are supported.
 License: Apache License (== 2.0)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)

R/app_ui.R

@@ -71,10 +71,10 @@ app_ui <- function(request) {
                       icon = icon("angles-right")),
           tags$li(class = "header", style = "color: grey; margin-top: 18px; margin-bottom: 10px; padding-left: 15px;", "Information"),
           menuItem("Source Code", icon = icon("circle-info"), href = "https://www.github.com/Breeding-Insight/Genomics_Shiny_App"),
-          menuItem(
-            span("Job Queue", bs4Badge("demo", position = "right", color = "warning")),
-            tabName = "slurm",
-            icon = icon("clock")),
+          #menuItem(
+          #  span("Job Queue", bs4Badge("demo", position = "right", color = "warning")),
+          #  tabName = "slurm",
+          #  icon = icon("clock")),
           menuItem("Help", tabName = "help", icon = icon("circle-question"))
         )
       ),
@@ -98,7 +98,7 @@ app_ui <- function(request) {
         ),
         left = div(
           style = "display: flex; align-items: center; height: 100%;",  # Center the version text vertically
-          "v0.6.2")
+          "v1.0.0")
       ),
       dashboardBody(
         disconnectMessage(), #Adds generic error message for any error if not already accounted for

R/mod_DosageCall.R

@@ -19,8 +19,9 @@ mod_DosageCall_ui <- function(id){
       fluidRow(
         box(
           title = "Inputs", status = "info", solidHeader = TRUE, collapsible = FALSE, collapsed = FALSE,
-          fileInput(ns("madc_file"), "Choose MADC or VCF File", accept = c(".csv",".vcf",".gz")),
-          fileInput(ns("madc_passport"), "Choose Passport File (optional)", accept = c(".csv")),
+          "* Required",
+          fileInput(ns("madc_file"), "Choose MADC or VCF File*", accept = c(".csv",".vcf",".gz")),
+          fileInput(ns("madc_passport"), "Choose Trait File", accept = c(".csv")),
           conditionalPanel(
             condition = "output.passportTablePopulated",
             ns = ns,
@@ -161,7 +162,7 @@ mod_DosageCall_server <- function(input, output, session, parent_session){
   # Update dropdown menu choices based on uploaded passport file
   passport_table <- reactive({
     validate(
-      need(!is.null(input$madc_passport), "Upload passport file to access results in this section."),
+      need(!is.null(input$madc_passport), "Upload Trait File to access results in this section."),
     )
     info_df <- read.csv(input$madc_passport$datapath, header = TRUE, check.names = FALSE)
     info_df[,1] <- as.character(info_df[,1]) #Makes sure that the sample names are characters instead of numeric

R/mod_GS.R

@@ -21,7 +21,7 @@ mod_GS_ui <- function(id){
       column(width = 3,
              box(title="Inputs", width = 12, collapsible = TRUE, collapsed = FALSE, status = "info", solidHeader = TRUE,
                  fileInput(ns("pred_known_file"), "Choose Training VCF File", accept = c(".csv",".vcf",".gz")),
-                 fileInput(ns("pred_trait_file"), "Choose Passport File", accept = ".csv"),
+                 fileInput(ns("pred_trait_file"), "Choose Trait File", accept = ".csv"),
                  fileInput(ns("pred_est_file"), "Choose Prediction VCF File", accept = c(".csv",".vcf",".gz")),
                  numericInput(ns("pred_est_ploidy"), "Species Ploidy", min = 1, value = NULL),
                  virtualSelectInput(

R/mod_GSAcc.R

@@ -21,7 +21,7 @@ mod_GSAcc_ui <- function(id){
       column(width = 3,
              box(title="Inputs", width = 12, collapsible = TRUE, collapsed = FALSE, status = "info", solidHeader = TRUE,
                  fileInput(ns("pred_file"), "Choose VCF File", accept = c(".csv",".vcf",".gz")),
-                 fileInput(ns("trait_file"), "Choose Passport File", accept = ".csv"),
+                 fileInput(ns("trait_file"), "Choose Trait File", accept = ".csv"),
                  numericInput(ns("pred_ploidy"), "Species Ploidy", min = 1, value = NULL),
                  numericInput(ns("pred_cv"), "Iterations", min = 1, max=20, value = 5),
                  virtualSelectInput(

R/mod_Home.R

@@ -20,17 +20,17 @@ mod_Home_ui <- function(id){
                box(
                  title = "Breeding Insight Genomics App", status = "info", solidHeader = FALSE, width = 12, collapsible = FALSE,
                  HTML(
-                   "<strong>The app is under development</strong>
-              <p>Breeding Insight provides bioinformatic processing support for our external collaborators. This R shiny app provides a web-based user friendly way for users to analyze genomic data without needing to use command-line tools.</p>
+              "<p>The BIGapp is a user-friendly tool for processing low to mid-density genotyping data for diploid and polyploid species. This R shiny app provides a web-based user friendly way for users to analyze genomic data without needing to use command-line tools.
+              Additional analysis will be added, with the initial focus on a core set of features for supporting breeding decisions.</p>
 
               <p><b>Supported Analyses</b></p>
               Initial supported analyses includes the mature genomics/bioinformatics pipelines developed within Breeding Insight:
               <ul>
-                <li>Genotype processing</li>
-                <li>Summary metrics</li>
+                <li>Genotype Processing</li>
+                <li>Summary Metrics</li>
                 <li>Population Structure</li>
                 <li>GWAS</li>
-                <li>GS</li>
+                <li>Genomic Selection</li>
               </ul>"
                  ),
                  style = "overflow-y: auto; height: 500px"

R/mod_PCA.R

@@ -26,7 +26,7 @@ mod_PCA_ui <- function(id){
                title = "Inputs", width = 12, solidHeader = TRUE, status = "info",
                p("* Required"),
                fileInput(ns("dosage_file"), "Choose VCF File*", accept = c(".csv",".vcf",".gz")),
-               fileInput(ns("passport_file"), "Choose Passport File (Sample IDs in first column)", accept = c(".csv")),
+               fileInput(ns("passport_file"), "Choose Trait File (IDs in first column)", accept = c(".csv")),
                #Dropdown will update after passport upload
                numericInput(ns("pca_ploidy"), "Species Ploidy*", min = 2, value = NULL),
                actionButton(ns("pca_start"), "Run Analysis"),
@@ -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"),hr(),
+                     downloadButton(ns('download_pheno'), "Download Trait Example File"),hr(),
                      actionButton(ns("pca_summary"), "Summary"),
                      circle = FALSE,
                      status = "warning",
@@ -46,9 +46,8 @@ mod_PCA_ui <- function(id){
              ),
              box(
                title = "Plot Controls", status = "warning", solidHeader = TRUE, collapsible = TRUE,collapsed = FALSE, width = 12,
-               "Change the PCA plot parameters", br(),
-               selectInput(ns('group_info'), label = 'Color Variable (eg, Taxon)', choices = NULL),
-               materialSwitch(ns('use_cat'), label = "Color Specific Category Within Variable?", status = "success"),
+               selectInput(ns('group_info'), label = 'Color Variable', choices = NULL),
+               materialSwitch(ns('use_cat'), label = "Color Category", status = "success"),
                conditionalPanel(condition = "input.use_cat",
                                 ns = ns,
                                 virtualSelectInput(
@@ -89,7 +88,7 @@ mod_PCA_ui <- function(id){
              )
       ),
       column(width = 8,
-             box(title = "Passport Data", width = 12, solidHeader = TRUE, collapsible = TRUE, status = "info", collapsed = FALSE, maximizable = T,
+             box(title = "Trait Data", width = 12, solidHeader = TRUE, collapsible = TRUE, status = "info", collapsed = FALSE, maximizable = T,
                  DTOutput(ns('passport_table')),
                  style = "overflow-y: auto; height: 480px"
              ),

R/mod_gwas.R

@@ -20,7 +20,7 @@ mod_gwas_ui <- function(id){
       column(width = 3,
              box(title="Inputs", width = 12, collapsible = TRUE, collapsed = FALSE, status = "info", solidHeader = TRUE,
                  fileInput(ns("gwas_file"), "Choose VCF File", accept = c(".csv",".vcf",".gz")),
-                 fileInput(ns("phenotype_file"), "Choose Passport File", accept = ".csv"),
+                 fileInput(ns("phenotype_file"), "Choose Trait File", accept = ".csv"),
                  numericInput(ns("gwas_ploidy"), "Species Ploidy", min = 1, value = NULL),
                  numericInput(ns("bp_window_before"), "Base pair window (Mb)", min = 0, value = 2),
                  selectInput(ns('gwas_threshold'), label='Significance Threshold Method', choices = c("M.eff","Bonferroni","FDR","permute"), selected="M.eff"),