inst/application/ui.R

In taylor-lab/facets-preview: Review and refit FACETS runs

#' helper function for app
#'
#' @return runs ui
#' @export ui
#' @importFrom shinyWidgets radioGroupButtons
#' @importFrom DT datatable
#' @import shinyjs
#' @import rhandsontable

## to keep the text boxes inline.
textInputRow<-function (inputId, label, value = "") {
  div(style="display:inline-block",
      tags$label(label, `for` = inputId), 
      tags$input(id = inputId, type = "text", value = value, class="input-group"))
}

ui <-
  fluidPage(
   shinyjs::useShinyjs(),
   tags$style(".glyphicon-ok-sign {color:#2b8ee5}
              .glyphicon-remove {color:darkred}
              .glyphicon-ok, .glyphicon-thumbs-up {color:green}
              .glyphicon-remove, .glyphicon-thumbs-down {color:darkred}"),
    navbarPage(
      "FACETS Preview",
      id="navbarPage1",
      tabPanel("Load Samples",
               value="tabPanel_sampleInput",
               mainPanel(
                 shinyjs::hidden(
                   wellPanel(id = "wellPanel_mountFail",
                             style = "background-color: white; border-color: white; ",
                             HTML(
                               paste0("<div style=\"font-size: 16px; font-family: georgia; color: red; display: inline-block\">
                                      <i class=\"fa fa-exclamation-triangle\" aria-hidden=\"true\"></i><strong> /juno/ not mounted. 
                                      Nothing is gonna work!  </strong></div>")
                             ),
                             actionButton("button_mountFailRefresh", "Check for mount again", icon = icon("refresh"))
                   )
                 ),
                 HTML(
                   "<div style=\"background-color: #EEEEEE; padding: 20px;font-size: 16px; \">
                   <strong>USAGE</strong> <br> Enter facets output directory for
                   each of the samples to be reviewed. This facets output directory is of the standard format generated by
                   facetsSuite v2. The directory should have the counts file as well as the one or many run directories
                   (eg: default, facets_c50p100R0.5.6, refit_dipLogR_1.0, etc)</div><br>"
                 ),
                 wellPanel(
                   h4("Load from selected repository. Note: Refit permissions maybe restricted."),
                   div(style="display:inline-block",
                       actionLink("link_choose_repo", "choose repository"),
                       style="align:right; padding:1px"),
                   h4(p(id = "element_repo_name", "No repository loaded!")),
                   h5(p(id = "element_repo_manifest", "")),
                   textAreaInput("textAreaInput_repoSamplesInput", label=NULL, value="", rows=1),
                   actionButton("button_repoSamplesInput", "Retrieve sample(s) from repo", class = "btn-primary")
                 ),
                 h3("or",style="text-align:center"),
                 wellPanel(
                   h4("Paste facets run directories"),
                   h5("Eg: /juno/work/ccs/bandlamc/facets_review_app/test_data/P-0009137-T01-IM5_P-0009137-N01-IM5"),
                   textAreaInput("textAreaInput_samplesInput", label=NULL, value="", rows=4),
                   actionButton("button_samplesInput", "Retrieve Sample(s)", class = "btn-primary")
                 ),
                 width = 12
                 )
      ),
      tabPanel("Samples Manifest",
               value="tabPanel_samplesManifest",
               mainPanel(
                 wellPanel(downloadLink("download_mapping_file", "Download Mapping File"), 
                           style = "background: gray90"),
                 wellPanel(DT::dataTableOutput("datatable_samples"), style = "background: gray90"),
                 width=12
               )
      ),
      tabPanel("Review Fits",
               value="tabPanel_reviewFits",
               fluidRow(
                 column(3,
                        wellPanel(
                          h4(strong("Select fit:")),
                          selectInput(inputId = "selectInput_selectFit", label=NULL,
                                      choices=c("Not selected"), selected=NA),
                          shinyjs::hidden(div(id="div_bestFitTrophy",
                                              HTML(" <center><font size=4>
                                                   <i class=\"fa fa-thumbs-up\" aria-hidden=\"true\"></i> Reviewed as best fit</center>
                                                   </font>"), 
                                              style="color: darkgreen; align: left; width: 70%")),
                          style = "padding-left: 5px; padding-top: 10px; padding-right: 5px"
                        ),
                        wellPanel(
                          h4(strong("Select run: ")),
                          shinyWidgets::radioGroupButtons(inputId = "radioGroupButton_fitType",
                                                          choices = c("Purity", "Hisens"),
                                                          selected=NA,
                                                          status = "primary",size = 'normal', width='100%',justified = TRUE),
                          actionButton("button_copyClipPath", "Copy path to clipboard",
                                       icon = icon("clipboard"),
                                       style="height:28px;font-size:8pt;vertical-align: middle; color:darkblue"),
                          h5(em('run parameters')),
                          verbatimTextOutput("verbatimTextOutput_runParams",placeholder = TRUE),
                          style = "padding: 10px; "
                        ),
                        wellPanel(
                          h4(strong("Generate a new fit:")),
                          shinyjs::hidden(div(id="div_watcherSuccess",
                                              HTML(" Watcher status: <i class=\"fa fa-check\" aria-hidden=\"true\"></i>"), style="color: green; padding-bottom: 10px")),
                          shinyjs::hidden(div(id="div_watcherFail",
                                              HTML(" Watcher status: <i class=\"fa fa-times\" aria-hidden=\"true\"></i>"), style="color: red; padding-bottom: 10px")),
                          column(12,
                                 textInput("textInput_newDipLogR", value = "","dipLogR ")),
                          column(6, 
                                 textInput("textInput_newPurityCval", value = 100, "purity cval "),
                                 textInput("textInput_newPurityMinNHet", "purity min nhet ")),
                          column(6, 
                                 textInput("textInput_newHisensCval", value = 50, "hisens cval "),
                                 textInput("textInput_newHisensMinNHet", "hisens min nhet ")),
                          column(12,
                                 textInput("textInput_newSnpWindowSize", "snp window size "),
                                 textInput("textInput_newNormalDepth", "normal depth "),
                                 selectInput("selectInput_newFacetsLib", "facets version:",
                                             c("use current run's facets version" = "use current run's facets version"))),
                          actionButton("button_refit", "Run", class = "btn-primary", width = '100%'),
                          style = "padding: 10px"
                        )
                 ),
                 column(9,
                        mainPanel(
                          tabsetPanel(
                            id="reviewTabsetPanel",
                            tabPanel("PNG image",
                                     value = "png_image_tabset",
                                     imageOutput("imageOutput_pngImage1")),
                            tabPanel("QC Summary",
                                     value = "tabPanel_QC",
                                      h3("Showing QC for:"),
                                      verbatimTextOutput("verbatimTextOutput_name_of_qc_fit"),
                                      h3("facets QC flags:"),
                                      h4(p(id = "element_facets_qc_version1", ""), 
                                         style="color: #de2e07; font-weight: bold; font-style: italic; padding-top: 0px; padding-bottom: 0px"),
                                      DT::dataTableOutput("datatable_QC_flags"),
                                      h3("QC metrics (NOTE: purity run):"),
                                      DT::dataTableOutput("datatable_QC_metrics")
                                     ),
                            tabPanel("Close Ups",
                                     value="closeup_tabset",
                                     wellPanel(
                                       textInput("textInput_geneForCloseup", label = NULL,
                                                 placeholder = "Hugo Symbol"),
                                       actionButton("button_closeUpView", "View Gene", class = "btn-primary",
                                                    width='100%')),
                                     plotOutput(outputId = "plotOutput_closeup", height="600px")
                                     ),
                            tabPanel("Segments",
                                     mainPanel(DT::dataTableOutput("datatable_cncf"), width=12)),
                            tabPanel("Segments (editable)",
                                     wellPanel(
                                       HTML(
                                         "<div style=\"padding: 1px;font-size: 14px; \">
                                         <u>Note:</u> This table is editable and 'Save Changes' button saves the edits to file ending 
                                         with .cncf.edited.txt. This '.cncf.edited.txt' file (if exists) will be loaded 
                                         automatically next time. (Only tcn/lcn/tcn.em/lcn.em are saved)</div><br>"
                                       ),
                                       actionButton("button_saveChanges", "Save changes to this file",
                                                    width='100%', class="btn-primary"),
                                       rhandsontable::rHandsontableOutput("editableSegmentsTable"))
 
                                     ),
                            tabPanel("Review notes",
                                     wellPanel(
                                       h4(strong("facets QC summary:")),
                                       h4(p(id = "element_facets_qc_version2", ""), 
                                          style="color: #de2e07; font-weight: bold; font-style: italic; padding-top: 0px; padding-bottom: 0px"),
                                       DT::dataTableOutput("datatable_fitReviews")
                                     ),
                                     wellPanel(
                                       h4(strong("Review History:")),
                                       DT::dataTableOutput("datatable_reviewHistory")
                                     ),
                                     wellPanel(
                                       h4(strong("Add Manual Review:")),
                                       radioButtons("radioButtons_reviewStatus", label=NULL,
                                                          c("Not Reviewed" = "not_reviewed",
                                                            "No fit available" = "reviewed_no_fit",
                                                            "Acceptable fit" = "reviewed_acceptable_fit",
                                                            "Best fit" = "reviewed_best_fit"),
                                                    inline=TRUE,
                                                    selected = "not_reviewed"),
                                       conditionalPanel(
                                         condition = "input.radioButtons_reviewStatus == 'reviewed_acceptable_fit' | input.radioButtons_reviewStatus == 'reviewed_best_fit'",
                                         h5(strong("Select best fit (applicable only if best fit selected):")),
                                         selectInput(inputId = "selectInput_selectBestFit", label=NULL,
                                                     choices=c("Not selected")),
                                         checkboxInput(inputId = "checkbox_purity_only", label = "Use purity run for CCF estimation", value = FALSE),
                                         checkboxInput(inputId = "checkbox_use_edited_cncf", label = "Use edited.cncf.txt", value = FALSE),
                                         textInput("textInput_purity", label = 'Use purity (only to be set when facets purity is NA/0.3):')
                                       ),
                                       h4(strong("Review Notes:")),
                                       textAreaInput("textAreaInput_reviewNote", label=NULL, value="", rows=1),
                                       h4(strong("Reviewed By:")),
                                       verbatimTextOutput("verbatimTextOutput_signAs"),
                                       actionButton("button_addReview", "Submit Review", class = "btn-primary", width='100%')
                                       )
                                  ),
                            tabPanel("cBioPortal")
                          ),width = '100%'
                      )
               )
      )
    ),
    tabPanel("[sessionInfo]",
             value="tabPanel_sessionInfo",
             mainPanel(
               verbatimTextOutput("verbatimTextOutput_sessionInfo")
             )
    )
  )
)