Added a panel for model building and visualisation

plotly_testing.R

+library(plotly)
 # plotly ----
 data("diamonds", package = 'ggplot2')
 diamonds

polyploid_vis/app.R

@@ -2,7 +2,7 @@
 # R Shiny Script
 # Author: Jonathan Kunst
 # Date created: 27-09-2021
-# Date updated: 27-09-2021
+# Date updated: 21-10-2021
 
 # Packages ----
 library(DT)
@@ -88,7 +88,7 @@ ui <-  fluidPage(
                             numericInput(inputId = 'IBD_core',
                                         label = 'Numbers of processing cores',
                                         min = 1,
-                                        value = 1,
+                                        value = detectCores() / 2,
                                         max = detectCores() - 2),
                             
                             # Estimate starter
@@ -255,15 +255,16 @@ server <- function(input, output, session) {
                                                 select_offspring = rv$select_offspring(),
                                                 multiplot = c(1, 1))
   )
-  
-  output$plot_haplo_imp <- renderPlot(visualiseHaplo(IBD_list = IBD_imp(),
-                                                     display_by = "name",
-                                                     linkage_group = 1,
-                                                     select_offspring = IBD_imp()[1]$offspring[3:11],
-                                                     multiplot = c(3, 3))
-  )
+  # 
+  # output$plot_haplo_imp <- renderPlot(visualiseHaplo(IBD_list = IBD_imp(),
+  #                                                    display_by = "name",
+  #                                                    linkage_group = 1,
+  #                                                    select_offspring = IBD_imp()[1]$offspring[3:11],
+  #                                                    multiplot = c(3, 3))
+  # )
 }
 
 
 # Run Shiny app example ----
-shinyApp(ui = ui, server = server)
\ No newline at end of file
+shinyApp(ui = ui, server = server)
+

polyqtlvis/R/app_server.R

@@ -14,4 +14,6 @@ app_server <- function( input, output, session ) {
   # IBD estimation ----
   mod_IBD_panel_server("IBD_panel_ui_1", rv = rv)
   
+  mod_model_panel_server("model_panel_ui_1", rv = rv)
+  
 }

polyqtlvis/R/app_ui.R

@@ -17,7 +17,10 @@ app_ui <- function(request) {
                # IBD panel ----
                tabPanel('IBD',
                         mod_IBD_panel_ui("IBD_panel_ui_1")
-                        )
+                        ),
+               # Model panel
+               tabPanel('Model',
+                        mod_model_panel_ui("model_panel_ui_1"))
       )
     )
 }

polyqtlvis/R/mod_import.R

@@ -27,7 +27,7 @@ mod_import_server <- function(id, rv, rvlab){
     observeEvent(input$file, {
       req(input$file)
       if(rvlab == 'snp'){
-        rv[[rvlab]] <- read.csv(input$file$datapath, row.names = 1)
+        rv[[rvlab]] <- as.matrix(read.csv(input$file$datapath, row.names = 1))
       } else {
       name <- input$file$name[1] # if multiple csv length too long
       extension <- tools::file_ext(name)

polyqtlvis/R/mod_model_panel.R

+#' model_panel UI Function
+#'
+#' @description A shiny Module.
+#'
+#' @param id,input,output,session Internal parameters for {shiny}.
+#'
+#' @noRd 
+#'
+#' @importFrom shiny NS tagList 
+mod_model_panel_ui <- function(id){
+  ns <- NS(id)
+  tagList(
+    sidebarLayout(
+      sidebarPanel(
+        tabsetPanel(
+          tabPanel('PolyqtlR'),
+          tabPanel('qtlpoly')
+        )
+      ),
+      mainPanel()
+    )
+  )
+}
+    
+#' model_panel Server Functions
+#'
+#' @noRd 
+mod_model_panel_server <- function(id, rv){
+  moduleServer( id, function(input, output, session){
+    ns <- session$ns
+ 
+  })
+}
+    
+## To be copied in the UI
+# mod_model_panel_ui("model_panel_ui_1")
+    
+## To be copied in the server
+# mod_model_panel_server("model_panel_ui_1")
+
+

polyqtlvis/dev/02_dev.R

@@ -16,13 +16,14 @@
 ## Dependencies ----
 ## Add one line by package you want to add as dependency
 usethis::use_package('polyqtlR')
+usethis::use_package('plotly')
 usethis::use_package('readr')
 usethis::use_package('parallel')
 usethis::use_package('tools')
 
 ## Add modules ----
 ## Create a module infrastructure in R/
-golem::add_module(name = "import_panel") # Name of the module
+golem::add_module(name = "model_panel") # Name of the module
 
 
 ## Add helper functions ----