inst/shiny/ui/ui_upload.R

In TBSignatureProfiler: Profile RA-Seq Data Using TB Pathway Signatures

shiny::tabPanel("Upload Data",
                tags$div(
                  class = "jumbotron", style = "background-color:#ededed",
                  tags$div(
                    class = "container",
                    shiny::h1("TB Signature Profiler"),
                    shiny::p("Score, compare and visualize gene signatures"),
                    )
                  ),
                shiny::sidebarPanel(
                  shiny::radioButtons("dat", "Select Data",
                                      choices = c("Sample Data" = "samp",
                                                  "Upload Data" = "updat")),
                  shiny::conditionalPanel(condition = "input.dat == 'samp'",
                                          shiny::radioButtons(
                                            "sampdat", "Sample Datasets",
                                            choices = c('TB HIV' = 'tbhiv',
                                                        'TB Indian' = 'tbind'),
                                            selected = NULL)),
                  shiny::conditionalPanel(
                    condition = "input.dat == 'updat'",
                    shiny::radioButtons("updattype", "Choose File Type",
                                        choices = c(
                                          'Tab Separated Text Files' = 'rawdat',
                                          'Summarized Experiment' = 'sumexp'),
                                        selected = NULL)),
                  shiny::hr(),
                  shiny::actionButton('upload', 'Upload')),
                shiny::mainPanel(
                  shiny::conditionalPanel(
                    condition = "input.dat == 'updat'",
                    shiny::conditionalPanel(
                      condition = "input.updattype == 'rawdat'",
                      shiny::column(width = 4,
                                    shiny::wellPanel(
                                      shiny::h4("Upload Count File"),
                                      shiny::fileInput(
                                        "countsfile",
                                        shiny::HTML(
                                          base::paste(
                                            "Input assay (eg. counts, required):",
                                            tags$span(style = "color:red", "*",
                                                      sep = ""))
                                          ),
                                        accept = c(
                                          "text/csv",
                                          "text/comma-separated-values",
                                          "text/tab-separated-values",
                                          "text/plain", ".csv", ".tsv"
                                          )
                                        )
                                      )
                                    ),
                      shiny::column(width = 4,
                                    shiny::wellPanel(
                                      shiny::h4("Upload Meta Data File"),
                                      shiny::fileInput(
                                        "metdatfile",
                                        shiny::HTML(
                                          base::paste(
                                            "Meta Data (eg. disease, required):",
                                            tags$span(style = "color:red", "*",
                                                      sep = ""))
                                          ),
                                        accept = c(
                                          "text/csv",
                                          "text/comma-separated-values",
                                          "text/tab-separated-values",
                                          "text/plain", ".csv", ".tsv"
                                          )
                                        )
                                      )
                                    ),
                      shiny::selectInput("datassay",
                                         label = "Input Assay Type:",
                                         choices = c("Counts" = "counts",
                                                     "Log Counts" = 'log',
                                                     "CPM" = 'cpm',
                                                     "Log CPM" = 'logcpm'))
                      ),
                    shiny::conditionalPanel(condition = "input.updattype == 'sumexp'",
                                            shiny::h3(
                                              "Choose an RDS Summarized Experiment file that contains a TBSignature Object:"
                                              ),
                                            shiny::fileInput(
                                              "rdsFile", "TBSignature RDS file:",
                                              accept = c(".rds", ".RDS")
                                              )
                                            )
                    ),
                  DT::dataTableOutput("counttable", width = 700)
                  )
                )