First version of CuReSPR app and sample data files are prepared

.Rbuildignore

@@ -1,2 +1,4 @@
 ^\.github$
 ^codecov\.yml$
+^.*\.Rproj$
+^\.Rproj\.user$

R/app.R

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+library(shiny)
+library(shinyWidgets)
+library(shinythemes)
+library(DT)
+# source("global.R")
+library(refund.shiny)
+options(shiny.maxRequestSize=100*1024^2)
+# Define UI ----
+ui <- navbarPage("CuReSPR", id = "main",
+                 theme = shinytheme("cerulean"),
+#----------------------- ui Data Upload ------------------------------------
+                 tabPanel("Data Upload",
+                          sidebarLayout(
+                            sidebarPanel(
+                              h4("Set group numbers"),
+                              numericInput("num",
+                                           label = "",
+                                           value = 0,
+                                           min = 0),
+                              conditionalPanel(
+                                condition = "input.num > '0'",
+                                hr(),
+                                h4("Assign group names to each group number"),
+                                uiOutput("textInputs"),
+                                checkboxInput("paired", label = "Select if the fastq files are paired-end"),
+                                actionButton("fastqupload", "Upload fastq files"),
+                              ),
+                              conditionalPanel(
+                                condition = "input.fastqupload",
+                                fileInput("upload",
+                                          label = "",
+                                          accept = c('.fastq','fastq.gz'),
+                                          multiple = TRUE) # This option does not work on older browsers, including Internet Explorer 9 and earlier.
+                              ),
+                            ),
+                            mainPanel(
+                              #DT::DTOutput("files"),
+                              tableOutput("selected_file_table"),
+                              textOutput("groups")
+                            )
+                          )
+                 ),
+#----------------------- ui Creating Count Matrix ---------------------------------------
+                 tabPanel("Count the sgRNAs",
+                          h4("testing counting"),
+                          fluidPage(
+                            sidebarPanel(
+                            )
+                          )
+                 ),
+#----------------------- ui Pre-proccessing ---------------------------------------
+                 tabPanel("Preproccessing",
+                          h4("testing counting"),
+                          fluidPage(
+                            sidebarPanel(
+                            )
+                          )
+                 ),
+#----------------------- ui Differential Analysis ---------------------------------------
+                 tabPanel("Differential Analysis",
+                          h4("testing counting"),
+                          fluidPage(
+                            sidebarPanel(
+                            )
+                          )
+                 ),
+#----------------------- ui Pathway Analysis ---------------------------------------
+                 tabPanel("Pathway Analysis",
+                          h4("testing counting"),
+                          fluidPage(
+                            sidebarPanel(
+                            )
+                          )
+                 ),
+)
+
+# Define server logic ----
+server <- function(input, output) {
+  #----- numericInput -----
+  n <- reactive({input$num})
+  output$textInputs <- renderUI({
+    textInputs <- lapply(1:n(), function(i) {
+      textInput(paste0("group", i),
+                label = paste0("Group ", i))
+    })
+    do.call(tagList, textInputs)
+  })
+
+  values <- reactive({unlist(lapply(1:n(), function(i) {
+    input[[paste0("group", i)]]}))})
+  output$groups <- renderText({
+    req(values())
+  })
+  # groups <- as.character(unlist(values))
+  #output$groups <- renderText(paste0("Groups are: ", values))
+
+
+#----- fileInput fastq files -----
+  # output$files <- DT::renderDT({
+  #   DT::datatable(input$upload, selection = c("single"))
+  # })
+  output$selected_file_table <- renderTable({
+    req(input$upload[,1:2])
+  })
+}
+# Run the app ----
+shinyApp(ui = ui, server = server)
+
+