diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..b09a0bc
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,47 @@
+FROM rocker/r-ver:4.4.2
+RUN apt-get update && apt-get install -y  cmake libz-dev libcurl4-openssl-dev libssl-dev
+RUN R -e 'install.packages("remotes")'
+RUN Rscript -e 'remotes::install_version("adegenet",upgrade="never", version = "2.1.10")'
+RUN Rscript -e 'remotes::install_version("curl",upgrade="never", version = "6.0.1")'
+RUN Rscript -e 'remotes::install_version("DT",upgrade="never", version = "0.33")'
+RUN Rscript -e 'remotes::install_version("dplyr",upgrade="never", version = "1.1.4")'
+RUN Rscript -e 'remotes::install_version("vcfR",upgrade="never", version = "1.15.0")'
+RUN Rscript -e 'remotes::install_version("ggplot2",upgrade="never", version = "3.5.1")'
+RUN Rscript -e 'remotes::install_version("tidyr",upgrade="never", version = "1.3.1")'
+RUN Rscript -e 'remotes::install_version("curl",upgrade="never", version = "6.0.1")'
+RUN Rscript -e 'remotes::install_version("shiny",upgrade="never", version = "1.9.1")'
+RUN Rscript -e 'remotes::install_version("config",upgrade="never", version = "0.3.2")'
+RUN Rscript -e 'remotes::install_version("bs4Dash",upgrade="never", version = "2.3.4")'
+RUN Rscript -e 'remotes::install_version("golem",upgrade="never", version = "0.5.1")'
+RUN Rscript -e 'remotes::install_version("purrr",upgrade="never", version = "1.0.2")'
+RUN Rscript -e 'remotes::install_version("markdown",upgrade="never", version = "1.13")'
+RUN Rscript -e 'remotes::install_version("scales",upgrade="never", version = "1.3.0")'
+RUN Rscript -e 'remotes::install_version("plotly",upgrade="never", version = "4.10.4")'
+RUN Rscript -e 'remotes::install_version("shinyWidgets",upgrade="never", version = "0.8.7")'
+RUN Rscript -e 'remotes::install_version("shinyjs",upgrade="never", version = "2.1.0")'
+RUN Rscript -e 'remotes::install_version("shinydisconnect",upgrade="never", version = "0.1.1")'
+RUN Rscript -e 'remotes::install_version("shinyalert",upgrade="never", version = "3.1.0")'
+RUN Rscript -e 'remotes::install_version("stringr",upgrade="never", version = "1.5.1")'
+RUN Rscript -e 'remotes::install_version("updog",upgrade="never", version = "2.1.5")'
+RUN Rscript -e 'remotes::install_version("AGHmatrix",upgrade="never", version = "2.1.4")'
+RUN Rscript -e 'remotes::install_version("factoextra",upgrade="never", version = "1.0.7")'
+RUN Rscript -e 'remotes::install_version("httr",upgrade="never", version = "1.4.7")'
+RUN Rscript -e 'remotes::install_version("future",upgrade="never", version = "1.34.0")'
+RUN Rscript -e 'remotes::install_version("shinycssloaders",upgrade="never", version = "1.1.0")'
+RUN Rscript -e 'remotes::install_version("RColorBrewer",upgrade="never", version = "1.1.3")'
+RUN Rscript -e 'remotes::install_version("tibble",upgrade="never", version = "3.2.1")'
+RUN Rscript -e 'remotes::install_version("rrBLUP",upgrade="never", version = "4.6.3")'
+RUN Rscript -e 'remotes::install_version("MASS",upgrade="never", version = "7.3.60.2")'
+RUN Rscript -e 'remotes::install_version("Matrix",upgrade="never", version = "1.7.0")'
+RUN Rscript -e 'remotes::install_version("matrixcalc",upgrade="never", version = "1.0.6")'
+RUN Rscript -e 'remotes::install_github("Breeding-Insight/BIGr",upgrade="never")'
+RUN Rscript -e 'remotes::install_github("jendelman/GWASpoly",upgrade="never")'
+
+RUN mkdir /build_zone
+ADD . /build_zone
+WORKDIR /build_zone
+RUN R -e 'remotes::install_local(upgrade="never")'
+RUN rm -rf /build_zone
+EXPOSE 80
+CMD R -e "options('shiny.port'=80,shiny.host='0.0.0.0');BIGapp::run_app()"
+
diff --git a/R/mod_DosageCall.R b/R/mod_DosageCall.R
index ed737b7..fd7e5cd 100644
--- a/R/mod_DosageCall.R
+++ b/R/mod_DosageCall.R
@@ -6,7 +6,6 @@
 #'
 #' @noRd
 #'
-#' @importFrom shinyjs enable disable useShinyjs
 #' @importFrom shiny NS tagList
 #' @importFrom future availableCores
 #' @importFrom bs4Dash renderValueBox
@@ -16,6 +15,7 @@
 mod_DosageCall_ui <- function(id){
   ns <- NS(id)
   tagList(
+    useShinyjs(),
     fluidPage(
       disconnectMessage(
         text = "An unexpected error occurred, please reload the application and check the input file(s).",
@@ -55,9 +55,9 @@ mod_DosageCall_ui <- function(id){
               )
             )
           ),
-          textInput(ns("output_name"), "Output File Name"),
-          numericInput(ns("ploidy"), "Species Ploidy", min = 1, value = NULL),
-          selectInput(ns("updog_model"), "Updog Model", choices = c("norm","hw","bb","s1","s1pp","f1","f1pp","flex","uniform"), selected = "norm"),
+          textInput(ns("output_name"), "Output File Name*"),
+          numericInput(ns("ploidy"), "Species Ploidy*", min = 1, value = NULL),
+          selectInput(ns("updog_model"), "Updog Model*", choices = c("norm","hw","bb","s1","s1pp","f1","f1pp","flex","uniform"), selected = "norm"),
           conditionalPanel(
             condition = "input.updog_model == 'f1' | input.updog_model == 'f1pp'",
             ns = ns,
@@ -65,12 +65,12 @@ mod_DosageCall_ui <- function(id){
               style = "padding-left: 20px;",  # Add padding/indentation
               textInput(
                 inputId = ns("parent1"),
-                label = "Enter parent1 ID:",
+                label = "Enter parent1 ID*:",
                 value = NULL
               ),
               textInput(
                 inputId = ns("parent2"),
-                label = "Enter parent2 ID:",
+                label = "Enter parent2 ID*:",
                 value = NULL
               )
             )
@@ -82,15 +82,14 @@ mod_DosageCall_ui <- function(id){
               style = "padding-left: 20px;",  # Add padding/indentation
               textInput(
                 inputId = ns("parent"),
-                label = "Enter parent ID:",
+                label = "Enter parent ID*:",
                 value = NULL
               )
             )
           ),
-          numericInput(ns("cores"), "Number of CPU Cores", min = 1, max = (future::availableCores() - 1), value = 1),
+          numericInput(ns("cores"), "Number of CPU Cores*", min = 1, max = (future::availableCores() - 1), value = 1),
           actionButton(ns("run_analysis"), "Run Analysis"),
-          useShinyjs(),
-          downloadButton(ns('download_updog_vcf'), "Download VCF File", class = "butt"),
+          uiOutput(ns('mybutton')),
 
           div(style="display:inline-block; float:right",dropdownButton(
             HTML("<b>Input files</b>"),
@@ -123,7 +122,6 @@ mod_DosageCall_ui <- function(id){
 #' @import vcfR
 #' @import updog
 #' @importFrom BIGr updog2vcf
-#' @importFrom shinyjs enable disable
 #' @import dplyr
 #'
 #' @noRd
@@ -207,8 +205,6 @@ mod_DosageCall_server <- function(input, output, session, parent_session){
     valueBox(snp_number(), "Markers in uploaded file", icon = icon("dna"), color = "info")
   })
 
-  disable("download_updog_vcf")
-
   ##This is for performing Updog Dosage Calling
   updog_out <- eventReactive(input$run_analysis,{
 
@@ -374,7 +370,7 @@ mod_DosageCall_server <- function(input, output, session, parent_session){
 
       return()
     }
-    
+
     if (nrow(matrices$ref_matrix) == 0 || nrow(matrices$size_matrix) == 0) {
       shinyalert(
         title = "Data Warning!",
@@ -390,7 +386,7 @@ mod_DosageCall_server <- function(input, output, session, parent_session){
         showCancelButton = FALSE,
         animation = TRUE
       )
-      
+
       return()
     }
 
@@ -410,14 +406,9 @@ mod_DosageCall_server <- function(input, output, session, parent_session){
   })
 
   # Only make available the download button when analysis is finished
-  observe({
-    if (!is.null(updog_out())) {
-      Sys.sleep(1)
-      # enable the download button
-      enable("download_updog_vcf")
-    } else {
-      disable("download_updog_vcf")
-    }
+  output$mybutton <- renderUI({
+    if(isTruthy(updog_out()))
+      downloadButton(ns("download_updog_vcf"), "Download VCF file", class = "butt")
   })
 
   output$download_updog_vcf <- downloadHandler(
@@ -426,6 +417,7 @@ mod_DosageCall_server <- function(input, output, session, parent_session){
       paste0(output_name, ".vcf.gz")
     },
     content = function(file) {
+
       #Save Updog output as VCF file
       temp <- tempfile()
       updog2vcf(
@@ -459,14 +451,14 @@ mod_DosageCall_server <- function(input, output, session, parent_session){
       ex <- system.file("iris_DArT_MADC.csv", package = "BIGapp")
       file.copy(ex, file)
     })
-  
+
   ##Summary Info
   dosage_summary_info <- function() {
     #Handle possible NULL values for inputs
     genotype_file_name <- if (!is.null(input$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$ploidy) else "Not selected"
-    
+
     #Print the summary information
     cat(
       "BIGapp Dosage Calling Summary\n",
@@ -493,7 +485,7 @@ mod_DosageCall_server <- function(input, output, session, parent_session){
       sep = ""
     )
   }
-  
+
   # Popup for analysis summary
   observeEvent(input$dosage_summary, {
     showModal(modalDialog(
@@ -509,8 +501,8 @@ mod_DosageCall_server <- function(input, output, session, parent_session){
       )
     ))
   })
-  
-  
+
+
   # Download Summary Info
   output$download_dosage_info <- downloadHandler(
     filename = function() {
diff --git a/R/mod_Filtering.R b/R/mod_Filtering.R
index 511bcc2..0803e9a 100644
--- a/R/mod_Filtering.R
+++ b/R/mod_Filtering.R
@@ -51,8 +51,7 @@ mod_Filtering_ui <- function(id){
                    )
                  ),
                  actionButton(ns("run_filters"), "Apply Filters"),
-                 useShinyjs(),
-                 downloadButton(ns("start_updog_filter"), "Download", icon = icon("download"), class = "butt"),
+                 uiOutput(ns("mybutton")),
                  div(style="display:inline-block; float:right",dropdownButton(
                    HTML("<b>Input files</b>"),
                    p(downloadButton(ns('download_vcf'),""), "VCF Example File"),
@@ -75,8 +74,7 @@ mod_Filtering_ui <- function(id){
              valueBoxOutput(ns("snp_removed_box"), width = NULL),
              box(title = "Plot Controls", status = "warning", solidHeader = TRUE, collapsible = TRUE,
                  sliderInput(ns("hist_bins"),"Histogram Bins", min = 1, max = 1200, value = c(50), step = 1), width = NULL,
-                 div(style="display:inline-block; float:left",dropdownButton(
-                   tags$h3("Save Image"),
+                 div(style="display:inline-block; float:left", dropdownButton(
                    selectInput(inputId = ns('filter_hist'), label = 'Figure', choices = c("Bias Histogram",
                                                                                           "OD Histogram",
                                                                                           "Prop_mis Histogram",
@@ -88,7 +86,7 @@ mod_Filtering_ui <- function(id){
                    sliderInput(inputId = ns('image_height'), label = 'Height', value = 5, min = 1, max = 20, step = 0.5),
                    downloadButton(ns("download_filter_hist"), "Save"),
                    circle = FALSE,
-                   status = "danger",
+                   status = "danger", label = "Save Image",
                    icon = icon("floppy-disk"), width = "300px",
                    tooltip = tooltipOptions(title = "Click to see inputs!")
                  ))
@@ -112,37 +110,37 @@ mod_Filtering_ui <- function(id){
 mod_Filtering_server <- function(input, output, session, parent_session){
 
   ns <- session$ns
-  
+
   # Help links
   observeEvent(input$goPar, {
     # change to help tab
     updatebs4TabItems(session = parent_session, inputId = "MainMenu",
                       selected = "help")
-    
+
     # select specific tab
     updateTabsetPanel(session = parent_session, inputId = "VCF_Filtering_tabset",
                       selected = "VCF_Filtering_par")
     # expand specific box
     updateBox(id = "VCF_Filtering_box", action = "toggle", session = parent_session)
   })
-  
+
   observeEvent(input$goRes, {
     # change to help tab
     updatebs4TabItems(session = parent_session, inputId = "MainMenu",
                       selected = "help")
-    
+
     # select specific tab
     updateTabsetPanel(session = parent_session, inputId = "VCF_Filtering_tabset",
                       selected = "VCF_Filtering_results")
     # expand specific box
     updateBox(id = "VCF_Filtering_box", action = "toggle", session = parent_session)
   })
-  
+
   observeEvent(input$goCite, {
     # change to help tab
     updatebs4TabItems(session = parent_session, inputId = "MainMenu",
                       selected = "help")
-    
+
     # select specific tab
     updateTabsetPanel(session = parent_session, inputId = "VCF_Filtering_tabset",
                       selected = "VCF_Filtering_cite")
@@ -177,8 +175,6 @@ mod_Filtering_server <- function(input, output, session, parent_session){
     )
   })
 
-  disable("start_updog_filter")
-
   output$din_tabs <- renderUI({
     tabBox(width =12, collapsible = FALSE, status = "info",
            id = "updog_tab", height = "600px",
@@ -351,17 +347,11 @@ mod_Filtering_server <- function(input, output, session, parent_session){
   })
 
   # Only make available the download button when analysis is finished
-  observe({
-    if (!is.null(vcf())) {
-      Sys.sleep(1)
-      # enable the download button
-      enable("start_updog_filter")
-    } else {
-      disable("start_updog_filter")
-    }
+  output$mybutton <- renderUI({
+    if(isTruthy(vcf()))
+      downloadButton(ns("start_updog_filter"), "Download VCF file", class = "butt")
   })
 
-
   #Updog filtering
   output$start_updog_filter <- downloadHandler(
     filename = function() {
@@ -671,13 +661,13 @@ mod_Filtering_server <- function(input, output, session, parent_session){
       ex <- system.file("iris_DArT_VCF.vcf.gz", package = "BIGapp")
       file.copy(ex, file)
     })
-  
+
   ##Summary Info
   filtering_summary_info <- function() {
     #Handle possible NULL values for inputs
     genotype_file_name <- if (!is.null(input$updog_rdata$name)) input$updog_rdata$name else "No file selected"
     selected_ploidy <- if (!is.null(input$filter_ploidy)) as.character(input$filter_ploidy) else "Not selected"
-    
+
     #Print the summary information
     cat(
       "BIGapp VCF Filtering Summary\n",
@@ -711,7 +701,7 @@ mod_Filtering_server <- function(input, output, session, parent_session){
       sep = ""
     )
   }
-  
+
   # Popup for analysis summary
   observeEvent(input$filtering_summary, {
     showModal(modalDialog(
@@ -727,8 +717,8 @@ mod_Filtering_server <- function(input, output, session, parent_session){
       )
     ))
   })
-  
-  
+
+
   # Download Summary Info
   output$download_filtering_info <- downloadHandler(
     filename = function() {
diff --git a/R/mod_GS.R b/R/mod_GS.R
index cf65eb8..8f25715 100644
--- a/R/mod_GS.R
+++ b/R/mod_GS.R
@@ -112,7 +112,7 @@ mod_GS_ui <- function(id){
                      downloadButton(ns("download_pred_results_file"), "Save Files")),
                    circle = FALSE,
                    status = "danger",
-                   icon = icon("floppy-disk"), width = "300px",
+                   icon = icon("floppy-disk"), width = "300px", label = "Save Image",
                    tooltip = tooltipOptions(title = "Click to see inputs!")
                  ))
              )
@@ -144,38 +144,38 @@ mod_GS_server <- function(input, output, session, parent_session){
     # change to help tab
     updatebs4TabItems(session = parent_session, inputId = "MainMenu",
                       selected = "help")
-    
+
     # select specific tab
     updateTabsetPanel(session = parent_session, inputId = "Genomic_Prediction_tabset",
                       selected = "Genomic_Prediction_par")
     # expand specific box
     updateBox(id = "Genomic_Prediction_box", action = "toggle", session = parent_session)
   })
-  
+
   observeEvent(input$goRes, {
     # change to help tab
     updatebs4TabItems(session = parent_session, inputId = "MainMenu",
                       selected = "help")
-    
+
     # select specific tab
     updateTabsetPanel(session = parent_session, inputId = "Genomic_Prediction_tabset",
                       selected = "Genomic_Prediction_results")
     # expand specific box
     updateBox(id = "Genomic_Prediction_box", action = "toggle", session = parent_session)
   })
-  
+
   observeEvent(input$goCite, {
     # change to help tab
     updatebs4TabItems(session = parent_session, inputId = "MainMenu",
                       selected = "help")
-    
+
     # select specific tab
     updateTabsetPanel(session = parent_session, inputId = "Genomic_Prediction_tabset",
                       selected = "Genomic_Prediction_cite")
     # expand specific box
     updateBox(id = "Genomic_Prediction_box", action = "toggle", session = parent_session)
   })
-  
+
   #Default model choices
   advanced_options_pred <- reactiveValues(
     pred_model = "GBLUP",
@@ -183,12 +183,12 @@ mod_GS_server <- function(input, output, session, parent_session){
     pred_est_file = NULL,
     ped_file = NULL
   )
-  
+
   pred_outputs <- reactiveValues(corr_output = NULL,
                                  comb_output = NULL,
                                  all_GEBVs = NULL,
                                  avg_GEBVs = NULL)
-  
+
   #List the ped file name if previously uploaded
   output$uploaded_file_name <- renderText({
     if (!is.null(advanced_options_pred$ped_file)) {
@@ -197,7 +197,7 @@ mod_GS_server <- function(input, output, session, parent_session){
       ""  # Return an empty string if no file has been uploaded
     }
   })
-  
+
   output$uploaded_file_name_pred <- renderText({
     if (!is.null(advanced_options_pred$pred_est_file)) {
       paste("Previously uploaded file:", advanced_options_pred$pred_est_file$name)
@@ -205,7 +205,7 @@ mod_GS_server <- function(input, output, session, parent_session){
       ""  # Return an empty string if no file has been uploaded
     }
   })
-  
+
   #UI popup window for input
   observeEvent(input$advanced_options_pred, {
     showModal(modalDialog(
@@ -254,9 +254,9 @@ mod_GS_server <- function(input, output, session, parent_session){
       )
     ))
   })
-  
-  
-  
+
+
+
   #Close popup window when user "saves options"
   observeEvent(input$save_advanced_options_pred, {
     advanced_options_pred$pred_model <- input$pred_model
@@ -264,10 +264,10 @@ mod_GS_server <- function(input, output, session, parent_session){
     advanced_options_pred$pred_est_file <- input$pred_est_file
     advanced_options_pred$ped_file <- input$ped_file
     # Save other inputs as needed
-    
+
     removeModal()  # Close the modal after saving
   })
-  
+
   ###Genomic Prediction
   #This tab involved 3 observeEvents
   #1) to get the traits listed in the phenotype file
@@ -283,7 +283,7 @@ mod_GS_server <- function(input, output, session, parent_session){
     updateVirtualSelect("pred_fixed_info2", choices = trait_var2, session = session)
     updateVirtualSelect("pred_trait_info2", choices = trait_var2, session = session)
   })
-  
+
   observeEvent(input$pred_fixed_info2, {
     updateVirtualSelect("pred_fixed_cat2", choices = input$pred_fixed_info2, session = session)
   })
@@ -592,22 +592,22 @@ mod_GS_server <- function(input, output, session, parent_session){
         }
       }
     )
-    
+
     #Status
     updateProgressBar(session = session, id = "pb_gp", value = 40, title = "Generating Matrices")
-    
+
     #Create relationship matrix depending on the input VCF files
     if (is.null(advanced_options_pred$pred_est_file)) {
       #Subset phenotype file by common IDs
       pheno2 <- pheno2[common_ids, ]
-      
+
       #Matrix
       Kin_mat <- A.mat(t(train_geno_adj_init), max.missing=NULL,impute.method="mean",return.imputed=FALSE)
-      
+
     } else{
       #Subset phenotype file and training file by common IDs
       pheno2 <- pheno2[common_ids, ]
-      
+
       #Match training and testing genotype file SNPs
       common_markers <- intersect(rownames(train_geno_adj_init), rownames(est_geno_adj_init))
       #first remove samples from training genotype matrix that are not in the phenotype file
@@ -615,10 +615,10 @@ mod_GS_server <- function(input, output, session, parent_session){
       #Merge the training and prediction genotype matrices
       est_geno_adj_init <- est_geno_adj_init[common_markers, ]
       train_pred_geno <- cbind(train_geno_adj, est_geno_adj_init)
-      
+
       #Matrix
       Kin_mat <- A.mat(t(train_pred_geno), max.missing=NULL,impute.method="mean",return.imputed=FALSE)
-      
+
     }
 
     #Save to reactive values
@@ -663,13 +663,13 @@ mod_GS_server <- function(input, output, session, parent_session){
 
     #Status
     updateProgressBar(session = session, id = "pb_gp", value = 90, title = "Generating Results")
-    
+
     #initialize dataframe
     results_GEBVs <- matrix(nrow = ncol(gmat), ncol = length(traits) + 1)
     results_TRAITs <- matrix(nrow = ncol(gmat), ncol = length(traits) + 1)
     colnames(results_TRAITs) <- c("Sample",paste0(traits))  # Set the column names to be the traits
     colnames(results_GEBVs) <- c("Sample",paste0(traits))  # Set the column names to be the traits
-    
+
     #GBLUP for each trait
     for (trait_idx in 1:length(traits)) {
       traitpred <- kin.blup(data = pheno2,
@@ -679,24 +679,24 @@ mod_GS_server <- function(input, output, session, parent_session){
                             covariate = fixed_cov,
                             K=gmat,
                             n.core = cores)
-      
+
       results_GEBVs[, (trait_idx+1)] <- traitpred$g
       results_TRAITs[, (trait_idx+1)] <- traitpred$pred
     }
     #Organize dataframes
     results_GEBVs[,1] <- row.names(data.frame(traitpred$g))
     results_TRAITs[,1] <- row.names(data.frame(traitpred$pred))
-    
+
     #Label the samples that already had phenotype information
     results_GEBVs <- data.frame(results_GEBVs)
     results_TRAITs <- data.frame(results_TRAITs)
     exists_in_df <- results_GEBVs[[1]] %in% pheno2[[1]]
     results_GEBVs <- cbind(results_GEBVs[1], "w/Pheno" = exists_in_df, results_GEBVs[-1])
     results_TRAITs <- cbind(results_TRAITs[1], "w/Pheno" = exists_in_df, results_TRAITs[-1])
-    
+
     #Status
     updateProgressBar(session = session, id = "pb_gp", value = 100, title = "Finished!")
-    
+
     ##Make output tables depending on 1 or 2 VCF/pedigree files used.
     #GEBVs
     if (!is.null(advanced_options_pred$pred_est_file)) {
@@ -705,7 +705,7 @@ mod_GS_server <- function(input, output, session, parent_session){
     } else{
       pred_outputs2$all_GEBVs <- results_GEBVs
     }
-    
+
     #BLUPs of genetic values
     if (!is.null(advanced_options_pred$pred_est_file)) {
       # Subset rows where 'w/Pheno' is FALSE and drop the 'w/Pheno' column
@@ -765,7 +765,7 @@ mod_GS_server <- function(input, output, session, parent_session){
       ex <- system.file("iris_passport_file.csv", package = "BIGapp")
       file.copy(ex, file)
     })
-  
+
   #Download files for GP
   output$download_pred_results_file <- downloadHandler(
     filename = function() {
@@ -780,21 +780,21 @@ mod_GS_server <- function(input, output, session, parent_session){
       ebv_file <- file.path(temp_dir, paste0("GS-EBV-predictions-", Sys.Date(), ".csv"))
       write.csv(pred_outputs2$all_GEBVs, ebv_file, row.names = FALSE)
       temp_files <- c(temp_files, ebv_file)
-      
+
       trait_file <- file.path(temp_dir, paste0("GS-Phenotype-predictions-", Sys.Date(), ".csv"))
       write.csv(pred_outputs2$trait_output, trait_file, row.names = FALSE)
       temp_files <- c(temp_files, trait_file)
-      
+
       # Zip files only if there's something to zip
       if (length(temp_files) > 0) {
         zip(file, files = temp_files, extras = "-j") # Using -j to junk paths
       }
-      
+
       # Optionally clean up
       file.remove(temp_files)
     }
   )
-  
+
   ##Summary Info
   pred_summary_info <- function() {
     # Handle possible NULL values for inputs
@@ -802,7 +802,7 @@ mod_GS_server <- function(input, output, session, parent_session){
     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",
@@ -836,7 +836,7 @@ mod_GS_server <- function(input, output, session, parent_session){
       sep = ""
     )
   }
-  
+
   # Popup for analysis summary
   observeEvent(input$pred_summary, {
     showModal(modalDialog(
@@ -852,8 +852,8 @@ mod_GS_server <- function(input, output, session, parent_session){
       )
     ))
   })
-  
-  
+
+
   # Download Summary Info
   output$download_pred_info <- downloadHandler(
     filename = function() {
diff --git a/R/mod_GSAcc.R b/R/mod_GSAcc.R
index 9df59b2..b80665d 100644
--- a/R/mod_GSAcc.R
+++ b/R/mod_GSAcc.R
@@ -30,13 +30,14 @@ 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 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),
+                 "* Required",
+                 fileInput(ns("pred_file"), "Choose VCF File*", accept = c(".csv",".vcf",".gz")),
+                 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(
                    inputId = ns("pred_trait_info"),
-                   label = "Select Trait(s):",
+                   label = "Select Trait(s)*:",
                    choices = NULL,
                    showValueAsTags = TRUE,
                    search = TRUE,
@@ -122,7 +123,7 @@ mod_GSAcc_ui <- function(id){
                      downloadButton(ns("download_pred_file"), "Save Files")),
                    circle = FALSE,
                    status = "danger",
-                   icon = icon("floppy-disk"), width = "300px",
+                   icon = icon("floppy-disk"), width = "300px", label = "Save Image",
                    tooltip = tooltipOptions(title = "Click to see inputs!")
                  ))
              )
@@ -154,31 +155,31 @@ mod_GSAcc_server <- function(input, output, session, parent_session){
     # change to help tab
     updatebs4TabItems(session = parent_session, inputId = "MainMenu",
                       selected = "help")
-    
+
     # select specific tab
     updateTabsetPanel(session = parent_session, inputId = "Predictive_Ability_tabset",
                       selected = "Predictive_Ability_par")
     # expand specific box
     updateBox(id = "Predictive_Ability_box", action = "toggle", session = parent_session)
   })
-  
+
   observeEvent(input$goRes, {
     # change to help tab
     updatebs4TabItems(session = parent_session, inputId = "MainMenu",
                       selected = "help")
-    
+
     # select specific tab
     updateTabsetPanel(session = parent_session, inputId = "Predictive_Ability_tabset",
                       selected = "Predictive_Ability_results")
     # expand specific box
     updateBox(id = "Predictive_Ability_box", action = "toggle", session = parent_session)
   })
-  
+
   observeEvent(input$goCite, {
     # change to help tab
     updatebs4TabItems(session = parent_session, inputId = "MainMenu",
                       selected = "help")
-    
+
     # select specific tab
     updateTabsetPanel(session = parent_session, inputId = "Predictive_Ability_tabset",
                       selected = "Predictive_Ability_cite")
@@ -834,14 +835,14 @@ 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",
@@ -874,7 +875,7 @@ mod_GSAcc_server <- function(input, output, session, parent_session){
       sep = ""
     )
   }
-  
+
   # Popup for analysis summary
   observeEvent(input$predAcc_summary, {
     showModal(modalDialog(
@@ -890,8 +891,8 @@ mod_GSAcc_server <- function(input, output, session, parent_session){
       )
     ))
   })
-  
-  
+
+
   # Download Summary Info
   output$download_predAcc_info <- downloadHandler(
     filename = function() {
diff --git a/R/mod_PCA.R b/R/mod_PCA.R
index 229e240..bc4869a 100644
--- a/R/mod_PCA.R
+++ b/R/mod_PCA.R
@@ -17,7 +17,7 @@ mod_PCA_ui <- function(id){
   ns <- NS(id)
   tagList(
     fluidPage(
-    # Add PCA content here
+      # Add PCA content here
       fluidRow(
         disconnectMessage(
           text = "An unexpected error occurred, please reload the application and check the input file(s).",
@@ -30,7 +30,7 @@ mod_PCA_ui <- function(id){
         ),
         useShinyjs(),
         inlineCSS(list(.borderred = "border-color: red", .redback = "background: red")),
-  
+
         column(width = 3,
                box(
                  title = "Inputs", width = 12, solidHeader = TRUE, status = "info",
@@ -42,23 +42,23 @@ mod_PCA_ui <- function(id){
                  br(),
                  actionButton(ns("pca_start"), "Run Analysis"),
                  div(style="display:inline-block; float:right",dropdownButton(
-                       HTML("<b>Input files</b>"),
-                       p(downloadButton(ns('download_vcf'),""), "VCF Example File"),
-                       p(downloadButton(ns('download_pheno'),""), "Trait Example File"), hr(),
-                       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(),
-                       actionButton(ns("pca_summary"), "Summary"),
-                       circle = FALSE,
-                       status = "warning",
-                       icon = icon("info"), width = "300px",
-                       tooltip = tooltipOptions(title = "Click to see info!")
-                     ))#,
+                   HTML("<b>Input files</b>"),
+                   p(downloadButton(ns('download_vcf'),""), "VCF Example File"),
+                   p(downloadButton(ns('download_pheno'),""), "Trait Example File"), hr(),
+                   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(),
+                   actionButton(ns("pca_summary"), "Summary"),
+                   circle = FALSE,
+                   status = "warning",
+                   icon = icon("info"), width = "300px",
+                   tooltip = tooltipOptions(title = "Click to see info!")
+                 ))#,
                  #style = "overflow-y: auto; height: 480px"
                ),
                box(
                  title = "Plot Controls", status = "warning", solidHeader = TRUE, collapsible = TRUE,collapsed = FALSE, width = 12,
-                 selectInput(ns('group_info'), label = 'Color Variable', choices = NULL),
+                 selectInput(ns('group_info'), label = 'Color Variable', choices = ""),
                  materialSwitch(ns('use_cat'), label = "Color Category", status = "success"),
                  conditionalPanel(condition = "input.use_cat",
                                   ns = ns,
@@ -94,7 +94,7 @@ mod_PCA_ui <- function(id){
                    downloadButton(ns("download_pca"), "Save Image"),
                    circle = FALSE,
                    status = "danger",
-                   icon = icon("floppy-disk"), width = "300px",
+                   icon = icon("floppy-disk"), width = "300px", label = "Save Image",
                    tooltip = tooltipOptions(title = "Click to see inputs!")
                  ))
                )
@@ -132,45 +132,45 @@ mod_PCA_ui <- function(id){
 mod_PCA_server <- function(input, output, session, parent_session){
 
   ns <- session$ns
-  options(warn = -1) #Uncomment to suppress warnings
-  
+  #options(warn = -1) #Uncomment to suppress warnings
+
   # Help links
   observeEvent(input$goPar, {
     # change to help tab
     updatebs4TabItems(session = parent_session, inputId = "MainMenu",
                       selected = "help")
-    
+
     # select specific tab
     updateTabsetPanel(session = parent_session, inputId = "PCA_tabset",
                       selected = "PCA_par")
     # expand specific box
     updateBox(id = "PCA_box", action = "toggle", session = parent_session)
   })
-  
+
   observeEvent(input$goRes, {
     # change to help tab
     updatebs4TabItems(session = parent_session, inputId = "MainMenu",
                       selected = "help")
-    
+
     # select specific tab
     updateTabsetPanel(session = parent_session, inputId = "PCA_tabset",
                       selected = "PCA_results")
     # expand specific box
     updateBox(id = "PCA_box", action = "toggle", session = parent_session)
   })
-  
+
   observeEvent(input$goCite, {
     # change to help tab
     updatebs4TabItems(session = parent_session, inputId = "MainMenu",
                       selected = "help")
-    
+
     # select specific tab
     updateTabsetPanel(session = parent_session, inputId = "PCA_tabset",
                       selected = "PCA_cite")
     # expand specific box
     updateBox(id = "PCA_box", action = "toggle", session = parent_session)
   })
-  
+
   #PCA reactive values
   pca_data <- reactiveValues(
     pc_df_pop = NULL,
@@ -329,7 +329,6 @@ mod_PCA_server <- function(input, output, session, parent_session){
     #PCA
     prin_comp <- prcomp(G.mat.updog, scale = TRUE)
     eig <- get_eigenvalue(prin_comp)
-    round(sum(eig$variance.percent[1:3]),1)
 
     ###Simple plots
     # Extract the PC scores
@@ -379,6 +378,7 @@ mod_PCA_server <- function(input, output, session, parent_session){
     pca_data$pc_df_pop <- pc_df_pop
     pca_data$variance_explained <- variance_explained
     pca_data$my_palette <- my_palette
+    pca_data$group_info <- input$group_info
 
     #End of PCA section
   })
@@ -390,10 +390,9 @@ mod_PCA_server <- function(input, output, session, parent_session){
       need(!is.null(pca_data$pc_df_pop), "Input Genotype file, Species ploidy, and run the analysis to access results in this section.")
     )
 
-
     # Generate colors
     if (!is.null(pca_data$my_palette)) {
-      unique_countries <- unique(pca_data$pc_df_pop[[input$group_info]])
+      unique_countries <- unique(pca_data$pc_df_pop[[pca_data$group_info]])
       palette <- brewer.pal(length(unique_countries), input$color_choice)
       my_palette <- colorRampPalette(palette)(length(unique_countries))
     } else {
@@ -413,21 +412,22 @@ mod_PCA_server <- function(input, output, session, parent_session){
     #Set factor
     if (!input$use_cat && is.null(my_palette)) {
       print("No Color Info")
-    }else{
-      pca_data$pc_df_pop[[input$group_info]] <- as.factor(pca_data$pc_df_pop[[input$group_info]])
+    } else {
+      if(pca_data$group_info != "") pca_data$pc_df_pop[[pca_data$group_info]] <- as.factor(pca_data$pc_df_pop[[pca_data$group_info]])
     }
 
     # Similar plotting logic here
 
+    #input$cat_color <- as.character(unique(pca_data$pc_df_pop[[input$group_info]]))
     cat_colors <- c(input$cat_color, "grey")
-    plot <- {if(!is.null(input$group_info) & input$group_info != "")
+    plot <- {if(!is.null(pca_data$group_info) & pca_data$group_info != "")
       ggplot(pca_data$pc_df_pop, aes(x = pca_data$pc_df_pop[[input$pc_X]],
                                      y = pca_data$pc_df_pop[[input$pc_Y]],
-                                     color = factor(pca_data$pc_df_pop[[input$group_info]]))) else
+                                     color = factor(pca_data$pc_df_pop[[pca_data$group_info]]))) else
                                        ggplot(pca_data$pc_df_pop, aes(x = pca_data$pc_df_pop[[input$pc_X]],
                                                                       y = pca_data$pc_df_pop[[input$pc_Y]]))} +
       geom_point(size = 2, alpha = 0.8) +
-      {if(input$use_cat) scale_color_manual(values = setNames(c(my_palette, "grey"), cat_colors), na.value = selected_grey) else
+      {if(input$use_cat & !is.null(my_palette)) scale_color_manual(values = setNames(c(my_palette, "grey"), cat_colors), na.value = selected_grey) else
         if(!is.null(my_palette)) scale_color_manual(values = my_palette)} +
       guides(color = guide_legend(override.aes = list(size = 5.5), nrow = 17)) +
       theme_minimal() +
@@ -441,7 +441,7 @@ mod_PCA_server <- function(input, output, session, parent_session){
       labs(
         x = paste0(input$pc_X, "(", pca_data$variance_explained[as.numeric(substr(input$pc_X, 3, 3))], "%)"),
         y = paste0(input$pc_Y, "(", pca_data$variance_explained[as.numeric(substr(input$pc_Y, 3, 3))], "%)"),
-        color = input$group_info
+        color = pca_data$group_info
       )
 
     plot  # Assign the plot to your reactiveValues
@@ -459,16 +459,22 @@ mod_PCA_server <- function(input, output, session, parent_session){
       need(!is.null(pca_data$pc_df_pop), "Input Genotype file, Species ploidy, and run the analysis to access results in this section.")
     )
 
+    tit = paste0('Total Explained Variance =', sum(pca_data$variance_explained[1:3]))
+
     #Generate colors
-    unique_countries <- unique(pca_data$pc_df_pop[[input$group_info]])
-    palette <- brewer.pal(length(unique_countries),input$color_choice)
-    my_palette <- colorRampPalette(palette)(length(unique_countries))
+    if(pca_data$group_info!= ""){
+      unique_countries <- unique(pca_data$pc_df_pop[[pca_data$group_info]])
+      palette <- brewer.pal(length(unique_countries),input$color_choice)
+      my_palette <- colorRampPalette(palette)(length(unique_countries))
 
-    tit = paste0('Total Explained Variance =', sum(pca_data$variance_explained[1:3]))
+      fig <- plot_ly(pca_data$pc_df_pop, x = ~PC1, y = ~PC2, z = ~PC3, color = as.factor(pca_data$pc_df_pop[[pca_data$group_info]]),
+                     colors = my_palette) %>%
+        add_markers(size = 12, text = paste0("Sample:",pca_data$pc_df_pop$Row.names))
 
-    fig <- plot_ly(pca_data$pc_df_pop, x = ~PC1, y = ~PC2, z = ~PC3, color = as.factor(pca_data$pc_df_pop[[input$group_info]]),
-                   colors = my_palette) %>%
-      add_markers(size = 12, text = paste0("Sample:",pca_data$pc_df_pop$Row.names))
+    } else {
+      fig <- plot_ly(pca_data$pc_df_pop, x = ~PC1, y = ~PC2, z = ~PC3) %>%
+        add_markers(size = 12, text = paste0("Sample:",pca_data$pc_df_pop$Row.names))
+    }
 
     fig <- fig %>%
       layout(
diff --git a/R/mod_dapc.R b/R/mod_dapc.R
index f221261..62690b4 100644
--- a/R/mod_dapc.R
+++ b/R/mod_dapc.R
@@ -87,7 +87,7 @@ mod_dapc_ui <- function(id){
                        downloadButton(ns("download_dapc_file"), "Save Files")),
                      circle = FALSE,
                      status = "danger",
-                     icon = icon("floppy-disk"), width = "300px",
+                     icon = icon("floppy-disk"), width = "300px", label = "Save Image",
                      tooltip = tooltipOptions(title = "Click to see inputs!")
                    ))
              ),
@@ -105,8 +105,7 @@ mod_dapc_ui <- function(id){
              bs4Dash::box(title = "DAPC Plots", status = "info", solidHeader = FALSE, width = 12, height = 550, maximizable = T,
                           bs4Dash::tabsetPanel(
                             tabPanel("BIC Plot",withSpinner(plotOutput(ns("BIC_plot"), height = '460px'))),
-                            tabPanel("DAPC Plot", withSpinner(plotOutput(ns("DAPC_plot"), height = '460px'))),
-                            tabPanel("STRUCTURE Plot", "Not yet supported"))
+                            tabPanel("DAPC Plot", withSpinner(plotOutput(ns("DAPC_plot"), height = '460px'))))
              )
       ),
       column(width = 1)
@@ -125,37 +124,37 @@ mod_dapc_ui <- function(id){
 mod_dapc_server <- function(input, output, session, parent_session){
 
   ns <- session$ns
-  
+
   # Help links
   observeEvent(input$goPar, {
     # change to help tab
     updatebs4TabItems(session = parent_session, inputId = "MainMenu",
                       selected = "help")
-    
+
     # select specific tab
     updateTabsetPanel(session = parent_session, inputId = "DAPC_tabset",
                       selected = "DAPC_par")
     # expand specific box
     updateBox(id = "DAPC_box", action = "toggle", session = parent_session)
   })
-  
+
   observeEvent(input$goRes, {
     # change to help tab
     updatebs4TabItems(session = parent_session, inputId = "MainMenu",
                       selected = "help")
-    
+
     # select specific tab
     updateTabsetPanel(session = parent_session, inputId = "DAPC_tabset",
                       selected = "DAPC_results")
     # expand specific box
     updateBox(id = "DAPC_box", action = "toggle", session = parent_session)
   })
-  
+
   observeEvent(input$goCite, {
     # change to help tab
     updatebs4TabItems(session = parent_session, inputId = "MainMenu",
                       selected = "help")
-    
+
     # select specific tab
     updateTabsetPanel(session = parent_session, inputId = "DAPC_tabset",
                       selected = "DAPC_cite")
@@ -193,7 +192,7 @@ mod_dapc_server <- function(input, output, session, parent_session){
       )
     }
     req(input$dosage_file$datapath, input$dapc_ploidy)
-    
+
     #PB
     updateProgressBar(session = session, id = "pb_dapc", value = 5, title = "Importing input files")
 
@@ -223,10 +222,10 @@ mod_dapc_server <- function(input, output, session, parent_session){
       genotypeMatrix <- apply(genotypeMatrix, 2, convert_to_dosage)
       rm(vcf) #Remove VCF
     }
-    
+
     #PB
     updateProgressBar(session = session, id = "pb_dapc", value = 30, title = "Calculating K")
-    
+
     #Perform analysis
     get_k <- findK(genotypeMatrix, maxK, ploidy)
 
@@ -234,10 +233,10 @@ mod_dapc_server <- function(input, output, session, parent_session){
     dapc_items$grp <- get_k$grp
     dapc_items$bestK <- get_k$bestK
     dapc_items$BIC <- get_k$BIC
-    
+
     #PB
     updateProgressBar(session = session, id = "pb_dapc", value = 100, title = "Step 1: Finished!")
-    
+
   })
 
   observeEvent(input$dapc_start, {
@@ -262,10 +261,10 @@ mod_dapc_server <- function(input, output, session, parent_session){
       )
     }
     req(input$dosage_file$datapath, input$dapc_ploidy, input$dapc_k)
-    
+
     #Pb
     updateProgressBar(session = session, id = "pb_dapc", value = 5, title = "Importing input files")
-    
+
     geno <- input$dosage_file$datapath
     ploidy <- as.numeric(input$dapc_ploidy)
     selected_K <- as.numeric(input$dapc_k)
@@ -278,10 +277,10 @@ mod_dapc_server <- function(input, output, session, parent_session){
 
     # Apply the function to the first INFO string
     info_ids <- extract_info_ids(info[1])
-    
+
     #Pb
     updateProgressBar(session = session, id = "pb_dapc", value = 30, title = "Formatting files")
-    
+
     #Get the genotype values if the updog dosage calls are present
     if ("UD" %in% info_ids) {
       genotypeMatrix <- extract.gt(vcf, element = "UD")
@@ -293,20 +292,20 @@ mod_dapc_server <- function(input, output, session, parent_session){
       genotypeMatrix <- apply(genotypeMatrix, 2, convert_to_dosage)
       rm(vcf) #Remove VCF
     }
-    
+
     #Pb
     updateProgressBar(session = session, id = "pb_dapc", value = 60, title = "Performing DAPC")
-    
+
     #Perform analysis
     clusters <- performDAPC(genotypeMatrix, selected_K, ploidy)
 
     #Assign results to reactive value
     dapc_items$assignments <- clusters$Q
     dapc_items$dapc <- clusters$dapc
-    
+
     #Pb
     updateProgressBar(session = session, id = "pb_dapc", value = 100, title = "Finished!")
-    
+
   })
 
   ###Outputs from DAPC
@@ -497,7 +496,7 @@ mod_dapc_server <- function(input, output, session, parent_session){
       ex <- system.file("iris_DArT_VCF.vcf.gz", package = "BIGapp")
       file.copy(ex, file)
     })
-  
+
   ##Summary Info
   dapc_summary_info <- function() {
     #Handle possible NULL values for inputs
diff --git a/R/mod_diversity.R b/R/mod_diversity.R
index 90295af..222e525 100644
--- a/R/mod_diversity.R
+++ b/R/mod_diversity.R
@@ -57,7 +57,7 @@ mod_diversity_ui <- function(id){
                      downloadButton(ns("download_div_file"), "Save Files")),
                    circle = FALSE,
                    status = "danger",
-                   icon = icon("floppy-disk"), width = "300px",
+                   icon = icon("floppy-disk"), width = "300px", label = "Save Image",
                    tooltip = tooltipOptions(title = "Click to see inputs!")
                  ))
              )
@@ -96,44 +96,44 @@ mod_diversity_ui <- function(id){
 mod_diversity_server <- function(input, output, session, parent_session){
 
     ns <- session$ns
-    
+
     # Help links
     observeEvent(input$goPar, {
       # change to help tab
       updatebs4TabItems(session = parent_session, inputId = "MainMenu",
                         selected = "help")
-      
+
       # select specific tab
       updateTabsetPanel(session = parent_session, inputId = "Genomic_Diversity_tabset",
                         selected = "Genomic_Diversity_par")
       # expand specific box
       updateBox(id = "Genomic_Diversity_box", action = "toggle", session = parent_session)
     })
-    
+
     observeEvent(input$goRes, {
       # change to help tab
       updatebs4TabItems(session = parent_session, inputId = "MainMenu",
                         selected = "help")
-      
+
       # select specific tab
       updateTabsetPanel(session = parent_session, inputId = "Genomic_Diversity_tabset",
                         selected = "Genomic_Diversity_results")
       # expand specific box
       updateBox(id = "Genomic_Diversity_box", action = "toggle", session = parent_session)
     })
-    
+
     observeEvent(input$goCite, {
       # change to help tab
       updatebs4TabItems(session = parent_session, inputId = "MainMenu",
                         selected = "help")
-      
+
       # select specific tab
       updateTabsetPanel(session = parent_session, inputId = "Genomic_Diversity_tabset",
                         selected = "Genomic_Diversity_cite")
       # expand specific box
       updateBox(id = "Genomic_Diversity_box", action = "toggle", session = parent_session)
     })
-    
+
     #######Genomic Diversity analysis
 
     #Genomic Diversity output files
@@ -255,11 +255,11 @@ mod_diversity_server <- function(input, output, session, parent_session){
       #Calculate PIC
       calc_allele_frequencies <- function(d_diplo_t, ploidy) {
         allele_frequencies <- apply(d_diplo_t, 1, function(x) {
-          count_sum <- sum(!is.na(x))  
-          allele_sum <- sum(x, na.rm = TRUE) 
+          count_sum <- sum(!is.na(x))
+          allele_sum <- sum(x, na.rm = TRUE)
           if (count_sum != 0) {allele_sum / (ploidy * count_sum)} else {NA}
         })
-        
+
         all_allele_frequencies <- data.frame(SNP = rownames(d_diplo_t), p1= allele_frequencies, p2= 1-allele_frequencies)
         return(all_allele_frequencies)
       }
@@ -271,19 +271,19 @@ mod_diversity_server <- function(input, output, session, parent_session){
         pic <- 1 - sum(freq_squared) - 2*upper_tri_sum
         return(pic)
       }
-      
+
       print(Fre[1:5,])
-      
+
       PIC_results <- apply(Fre[, c("p1", "p2")], 1, calc_pic)
       PIC_df <- data.frame(SNP_ID = Fre$SNP, PIC = PIC_results)
       rownames(PIC_df) <- NULL
-      
+
       print(PIC_df[1:5,])
       print(diversity_items$maf_df[1:5,])
-      
+
       diversity_items$snp_stats <- (merge(diversity_items$maf_df, PIC_df, by = "SNP_ID", all = TRUE))[,c("SNP_ID","MAF","PIC")]
       colnames(diversity_items$snp_stats)[1] <- "SNP"
-      
+
       #Updating value boxes
       output$mean_het_box <- renderValueBox({
         valueBox(
@@ -410,7 +410,9 @@ mod_diversity_server <- function(input, output, session, parent_session){
       validate(
         need(!is.null(diversity_items$het_df), "Input VCF, define parameters and click `run analysis` to access results in this session.")
       )
-      diversity_items$het_df
+      tb <- diversity_items$het_df
+      tb$Ho <- round(tb$Ho,4)
+      tb
     })
 
     output$sample_table <- renderDT({sample_table()}, options = list(scrollX = TRUE,autoWidth = FALSE, pageLength = 5))
@@ -419,7 +421,10 @@ mod_diversity_server <- function(input, output, session, parent_session){
       validate(
         need(!is.null(diversity_items$snp_stats), "Input VCF, define parameters and click `run analysis` to access results in this session.")
       )
-      diversity_items$snp_stats
+      tb <- diversity_items$snp_stats
+      tb$PIC <- round(tb$PIC,4)
+      tb$MAF <- round(tb$MAF,4)
+      tb
     })
 
     output$snp_table <- renderDT({snp_table()}, options = list(scrollX = TRUE,autoWidth = FALSE, pageLength = 5))
@@ -510,13 +515,13 @@ mod_diversity_server <- function(input, output, session, parent_session){
         ex <- system.file("iris_DArT_VCF.vcf.gz", package = "BIGapp")
         file.copy(ex, file)
       })
-    
+
     ##Summary Info
     diversity_summary_info <- function() {
       # Handle possible NULL values for inputs
       dosage_file_name <- if (!is.null(input$diversity_file$name)) input$diversity_file$name else "No file selected"
       selected_ploidy <- if (!is.null(input$diversity_ploidy)) as.character(input$diversity_ploidy) else "Not selected"
-      
+
       # Print the summary information
       cat(
         "BIGapp Summary Metrics Summary\n",
@@ -541,7 +546,7 @@ mod_diversity_server <- function(input, output, session, parent_session){
         sep = ""
       )
     }
-    
+
     # Popup for analysis summary
     observeEvent(input$diversity_summary, {
       showModal(modalDialog(
@@ -557,8 +562,8 @@ mod_diversity_server <- function(input, output, session, parent_session){
         )
       ))
     })
-    
-    
+
+
     # Download Summary Info
     output$download_diversity_info <- downloadHandler(
       filename = function() {
diff --git a/R/mod_dosage2vcf.R b/R/mod_dosage2vcf.R
index 2c8c879..cbac21f 100644
--- a/R/mod_dosage2vcf.R
+++ b/R/mod_dosage2vcf.R
@@ -41,7 +41,6 @@ mod_dosage2vcf_ui <- function(id){
             ),
             textInput(ns("d2v_output_name"), "Output File Name"),
             numericInput(ns("dosage2vcf_ploidy"), "Species Ploidy", min = 1, value = NULL),
-            #actionButton(ns("run_analysis"), "Run Analysis"),
             useShinyjs(),
             downloadButton(ns('download_d2vcf'), "Download VCF File", class = "butt"),
             div(style="display:inline-block; float:right",dropdownButton(
@@ -59,7 +58,7 @@ mod_dosage2vcf_ui <- function(id){
             ))
           )
       ),
-      column(width = 4,  
+      column(width = 4,
         valueBoxOutput(ns("ReportSnps"), width=12),
         box(title = "Status", width = 12, collapsible = TRUE, status = "info",
             progressBar(id = ns("dosage2vcf_pb"), value = 0, status = "info", display_pct = TRUE, striped = TRUE, title = " ")
@@ -126,45 +125,6 @@ mod_dosage2vcf_server <- function(input, output, session, parent_session){
     valueBox(snp_number(), "Number of Markers", icon = icon("dna"), color = "info")
   })
 
-  observeEvent(input$run_analysis, {
-    # Missing input with red border and alerts
-    toggleClass(id = "d2v_output_name", class = "borderred", condition = (is.na(input$d2v_output_name) | is.null(input$d2v_output_name) | input$d2v_output_name == ""))
-    toggleClass(id = "dosage2vcf_ploidy", class = "borderred", condition = (is.na(input$dosage2vcf_ploidy) | is.null(input$dosage2vcf_ploidy) | input$dosage2vcf_ploidy == ""))
-
-    if (is.null(input$report_file$datapath) | is.null(input$counts_file$datapath)) {
-      shinyalert(
-        title = "Missing input!",
-        text = "Upload Dose Report and Counts Files",
-        size = "s",
-        closeOnEsc = TRUE,
-        closeOnClickOutside = FALSE,
-        html = TRUE,
-        type = "error",
-        showConfirmButton = TRUE,
-        confirmButtonText = "OK",
-        confirmButtonCol = "#004192",
-        showCancelButton = FALSE,
-        animation = TRUE
-      )
-    }
-    req(input$report_file, input$counts_file, input$d2v_output_name, input$dosage2vcf_ploidy)
-
-    updateProgressBar(session = session, id = "dosage2vcf_pb", value = 10, title = "Input files evaluated.")
-
-    dosage_file_df <- read.csv(input$report_file$datapath)
-    snp_number <- length(dosage_file_df$X.[-c(1:7)])
-
-    #SNP counts value box
-    output$ReportSnps <- renderValueBox({
-      valueBox(snp_number, "Number of Markers", icon = icon("dna"), color = "info")
-    })
-
-    enable("download_d2vcf")
-
-    updateProgressBar(session = session, id = "dosage2vcf_pb", value = 100, title = "Click in Download to continue.")
-
-  })
-
   output$download_dose <- downloadHandler(
     filename = function() {
       paste0("BIGapp_Dose_Report_Example_file.csv")
@@ -191,8 +151,24 @@ mod_dosage2vcf_server <- function(input, output, session, parent_session){
     },
     content = function(file) {
       # Ensure the files are uploaded
+      # Missing input with red border and alerts
+      if (is.null(input$report_file$datapath) | is.null(input$counts_file$datapath) | input$d2v_output_name == "" | input$dosage2vcf_ploidy == "") {
+        shinyalert(
+          title = "Missing input!",
+          text = "Upload Dose Report and Counts Files",
+          size = "s",
+          closeOnEsc = TRUE,
+          closeOnClickOutside = FALSE,
+          html = TRUE,
+          type = "error",
+          showConfirmButton = TRUE,
+          confirmButtonText = "OK",
+          confirmButtonCol = "#004192",
+          showCancelButton = FALSE,
+          animation = TRUE
+        )
+      }
       req(input$report_file, input$counts_file, input$d2v_output_name, input$dosage2vcf_ploidy)
-
       # Get the uploaded file paths
       dosage_file <- input$report_file$datapath
       counts_file <- input$counts_file$datapath
@@ -251,14 +227,14 @@ mod_dosage2vcf_server <- function(input, output, session, parent_session){
       updateProgressBar(session = session, id = "dosage2vcf_pb", value = 100, title = "Complete! - Downloading VCF")
     }
   )
-  
+
   ##Summary Info
   d2vcf_summary_info <- function() {
     #Handle possible NULL values for inputs
     report_file_name <- if (!is.null(input$report_file$name)) input$report_file$name else "No file selected"
     counts_file_name <- if (!is.null(input$counts_file$name)) input$counts_file$name else "No file selected"
     selected_ploidy <- if (!is.null(input$dosage2vcf_ploidy)) as.character(input$dosage2vcf_ploidy) else "Not selected"
-    
+
     #Print the summary information
     cat(
       "BIGapp Dosage2VCF Summary\n",
@@ -282,7 +258,7 @@ mod_dosage2vcf_server <- function(input, output, session, parent_session){
       sep = ""
     )
   }
-  
+
   # Popup for analysis summary
   observeEvent(input$d2vcf_summary, {
     showModal(modalDialog(
@@ -298,8 +274,8 @@ mod_dosage2vcf_server <- function(input, output, session, parent_session){
       )
     ))
   })
-  
-  
+
+
   # Download Summary Info
   output$download_d2vcf_info <- downloadHandler(
     filename = function() {
diff --git a/R/mod_gwas.R b/R/mod_gwas.R
index 999a634..c712e74 100644
--- a/R/mod_gwas.R
+++ b/R/mod_gwas.R
@@ -29,21 +29,22 @@ 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 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', choices = c("M.eff","Bonferroni","FDR","permute"), selected="M.eff"),
-                 selectInput(ns('trait_info'), label = 'Select Trait', choices = NULL),
+                 "* Required",
+                 fileInput(ns("gwas_file"), "Choose VCF File*", accept = c(".csv",".vcf",".gz")),
+                 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*', choices = c("M.eff","Bonferroni","FDR","permute"), selected="M.eff"),
+                 selectInput(ns('trait_info'), label = 'Select Trait*', choices = NULL),
                  virtualSelectInput(
                    inputId = ns("fixed_info"),
-                   label = "Select Fixed Effects (optional):",
+                   label = "Select Fixed Effects:",
                    choices = NULL,
                    showValueAsTags = TRUE,
                    search = TRUE,
                    multiple = TRUE
                  ),
-                 sliderInput(ns("cores"), "Number of CPU Cores", min = 1, max = (availableCores() - 1), value = 1, step = 1),
+                 sliderInput(ns("cores"), "Number of CPU Cores*", min = 1, max = (availableCores() - 1), value = 1, step = 1),
                  actionButton(ns("gwas_start"), "Run Analysis"),
                  div(style="display:inline-block; float:right",dropdownButton(
                    HTML("<b>Input files</b>"),
@@ -128,7 +129,7 @@ mod_gwas_ui <- function(id){
                      downloadButton(ns("download_gwas_file"), "Save Files")),
                    circle = FALSE,
                    status = "danger",
-                   icon = icon("floppy-disk"), width = "300px",
+                   icon = icon("floppy-disk"), width = "300px", label = "Save Image",
                    tooltip = tooltipOptions(title = "Click to see inputs!")
                  ))
              )
@@ -150,7 +151,7 @@ mod_gwas_ui <- function(id){
 mod_gwas_server <- function(input, output, session, parent_session){
 
   ns <- session$ns
-  
+
   # Help links
   observeEvent(input$goGWASpar, {
     # change to help tab
@@ -493,7 +494,7 @@ mod_gwas_server <- function(input, output, session, parent_session){
         model <- c("additive","1-dom","2-dom","general","diplo-general","diplo-additive")
         updateSelectInput(session, "model_select", choices = c("all", model))
       }else{
-        model <- c("additive", "1-dom")
+        model <- c("additive", "1-dom", "general")
         updateSelectInput(session, "model_select", choices = c("all", model))
       }
 
@@ -508,7 +509,9 @@ mod_gwas_server <- function(input, output, session, parent_session){
       manhattan_plot_list <- list()
 
       #plot for six models per trait
-      manhattan_plot_list[["all"]] <- manhattan.plot(data2,traits=colnames(data@pheno[i]), models = model)+geom_point(size=3)+theme(text = element_text(size = 25),strip.text = element_text(face = "bold"))
+      manhattan_plot_list[["all"]] <- manhattan.plot(data2,traits=colnames(data@pheno[i]), models = model)+
+        geom_point(size=3)+
+        theme(text = element_text(size = 25),strip.text = element_text(face = "bold"), axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))
 
       #Status
       updateProgressBar(session = session, id = "pb_gwas", value = 80, title = "GWAS Complete: Now Plotting Results")
@@ -542,7 +545,7 @@ mod_gwas_server <- function(input, output, session, parent_session){
     #Status
     updateProgressBar(session = session, id = "pb_gwas", value = 100, status = "success", title = "Finished")
   })
-  
+
   #Checking if any QTLs were detected and returning a user notice if not
   observe({
     req(gwas_vars$gwas_df)
@@ -562,7 +565,7 @@ mod_gwas_server <- function(input, output, session, parent_session){
         animation = TRUE
       )
     }
-    
+
     #Gracefully abort
     return()
   })
@@ -615,7 +618,7 @@ mod_gwas_server <- function(input, output, session, parent_session){
 
   observe({
     req(gwas_vars$gwas_df_filt, nrow(gwas_vars$gwas_df_filt) > 0)
-    
+
     df <- gwas_vars$gwas_df_filt %>% filter(Model %in% input$sele_models)
     updatePickerInput(session = session, inputId = "sele_qtl", choices = unique(paste0(df$Marker, "_", df$Model)),
                       selected = unique(paste0(df$Marker, "_", df$Model)))
@@ -741,21 +744,21 @@ mod_gwas_server <- function(input, output, session, parent_session){
       # Temporary files list
       temp_dir <- tempdir()
       temp_files <- c()
-      
+
       if (!is.null(gwas_vars$gwas_df)) {
         # Create a temporary file for assignments
         gwas_file <- file.path(temp_dir, paste0("QTL-Significant_Markers-statistics-", Sys.Date(), ".csv"))
         write.csv(gwas_vars$gwas_df, gwas_file, row.names = FALSE)
         temp_files <- c(temp_files, gwas_file)
       }
-      
+
       if (!is.null(gwas_vars$gwas_df_filt)) {
         # Create a temporary file for assignments
         gwas_file <- file.path(temp_dir, paste0("QTL-LD-filtered-statistics-", Sys.Date(), ".csv"))
         write.csv(gwas_vars$gwas_df_filt, gwas_file, row.names = FALSE)
         temp_files <- c(temp_files, gwas_file)
       }
-      
+
       if (!is.null(gwas_vars$fit_qtl)) {
         # Create a temporary file for assignments
         gwas_file <- file.path(temp_dir, paste0("Multiple-QTL-model-statistics-", Sys.Date(), ".csv"))
@@ -813,7 +816,7 @@ mod_gwas_server <- function(input, output, session, parent_session){
         req(gwas_vars$LD_plot)
         #Plot
         print(gwas_vars$LD_plot)
-      
+
       } else if (input$gwas_figures == "Manhattan Plot") {
         req(gwas_vars$manhattan_plots, input$model_select)
         #Plot
diff --git a/inst/CITATION b/inst/CITATION
new file mode 100644
index 0000000..4fd7290
--- /dev/null
+++ b/inst/CITATION
@@ -0,0 +1,33 @@
+bibentry(bibtype    = "Article",
+         title      = "BIGapp: A User-Friendly Genomic Tool Kit Identified Quantitative Trait Loci for Creeping Rootedness in Alfalfa (Medicago sativa L.)",
+         year       = "TBD",
+         journal    = "TBD",
+         publisher  = "TBD",
+         volume     = "TBD",
+	       number     = "TBD",
+	       pages      = "TBD",
+	       issn       = "TBD",
+         doi        = "TBD",
+         author     = c(person(given  = "Alex",
+                               family = "Sandercock",
+                               email  = "ams866@cornell.edu"),
+                        person(given  = "Michael",
+                               family = "Peel"),
+                        person(given  = "Cristiane",
+                               family = "Taniguti"),
+                        person(given  = "Josue",
+                               family = "Chinchilla-Vargas"),
+                        person(given  = "Shufen",
+                               family = "Chen"),
+                        person(given  = "Manoj",
+                               family = "Sapkota"),
+                        person(given  = "Meng",
+                               family = "Lin"),
+                        person(given  = "Dongyan",
+                               family = "Zhao"),
+                        person(given  = "Craig",
+                               family = "Beil"),
+                        person(given  = "Moira",
+                               family = "Sheehan")
+                       )
+         )