Merge branch 'main' into svg_add

Breeding-Insight · Feb 7, 2025 · 8d2730c · 8d2730c
2 parents 69f56fc + 1b19bad
commit 8d2730c
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -67,6 +67,7 @@ Imports:
     markdown
 Remotes:
     github::jendelman/GWASpoly,
-    github::Breeding-Insight/BIGr
+    github::Breeding-Insight/BIGr,
+    bioc::release/Rsamtools
 Suggests:
     testthat
diff --git a/Dockerfile 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/NAMESPACE b/NAMESPACE
@@ -29,6 +29,7 @@ importFrom(MASS,ginv)
 importFrom(Matrix,nearPD)
 importFrom(R.utils,gunzip)
 importFrom(RColorBrewer,brewer.pal)
+importFrom(Rsamtools,bgzip)
 importFrom(adegenet,"pop<-")
 importFrom(adegenet,dapc)
 importFrom(adegenet,find.clusters)

diff --git 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).",
@@ -134,8 +134,7 @@ mod_DosageCall_ui <- function(id){
             )
           ),
           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>"),
@@ -167,7 +166,6 @@ mod_DosageCall_ui <- function(id){
 #' @import vcfR
 #' @import updog
 #' @importFrom BIGr updog2vcf
-#' @importFrom shinyjs enable disable
 #' @import dplyr
 #'
 #' @noRd
@@ -254,6 +252,7 @@ mod_DosageCall_server <- function(input, output, session, parent_session){
   disable("download_updog_vcf")
 
   ##This is for performing Dosage Calling
+
   updog_out <- eventReactive(input$run_analysis,{
     # Updog
     if (input$Rpackage == "Updog") {
@@ -469,14 +468,9 @@ 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(
@@ -490,6 +484,7 @@ mod_DosageCall_server <- function(input, output, session, parent_session){
 
     },
     content = function(file) {
+
       #Save Updog output as VCF file
       temp <- tempfile()
       if (input$Rpackage == "Updog") {
@@ -537,14 +532,14 @@ mod_DosageCall_server <- function(input, output, session, parent_session){
       ex <- system.file("iris_DArT_MADC.csv", package = "BIGapp")
       file.copy(ex, file)
     })
-  
+
   ##Summary Info
   dosage_summary_info <- function() {
     #Handle possible NULL values for inputs
     genotype_file_name <- if (!is.null(input$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$ploidy) else "Not selected"
-    
+
     #Print the summary information
     cat(
       "BIGapp Dosage Calling Summary\n",
@@ -572,7 +567,7 @@ mod_DosageCall_server <- function(input, output, session, parent_session){
       sep = ""
     )
   }
-  
+
   # Popup for analysis summary
   observeEvent(input$dosage_summary, {
     showModal(modalDialog(
@@ -588,8 +583,8 @@ 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
@@ -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",
                    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() {