R/loadDataTab.R

In SRHilz/GliomaAtlas3D: A 3D Map of Tumor-Wide Genetic and Microenvironmental Heterogeneity Present Across Adult Diffuse Glioma

#' UI-elements for data tab
#'
#' @import shiny
#' @import rgl
#' @importFrom utils packageVersion
#' @export 

loadDataTab <- function(){
    addResourcePath('www',system.file('shinyApp/www',package = "GliomaAtlas3D"))  
    dataTab <- tabPanel(title = "Explore", id = "data",
           
    sidebarLayout(
      sidebarPanel(
        
        # User input - select patient subset
        checkboxGroupInput("patientSubset", 
                           label = "Filter patients by tumor type", 
                           choices = list("IDH-mut" = 1, 
                                          "IDH-wt" = 2,
                                          "codel" = 3,
                                          "non-codel" = 4,
                                          "grade II or III" = 5,
                                          "grade IV" = 6,
                                          "newly diagnosed" = 7,
                                          "recurrent" = 8),
                           selected = c(1,2,3,4,5,6,7,8)),
        
        
        # CN instead of "Copy Number" bc of rds naming convention (need to change later)
        # User input - select patient
        uiOutput("patientUI"),
        
        htmlOutput("patientInfoUI"),
        
        # User input - select tumor (here just for future - for now all is done via patient because have 1 tumor per patient)
        uiOutput("tumorUI"),
        
        # User input - select dataset
        uiOutput("datasetUI"),
        
        # User input - select type ID (type of histological data)
        uiOutput("typeUI"),
        
        # User input - select copy number threshold
        uiOutput("thresholdUI"),
        
        # User input - select row if data has more than one 
        uiOutput("rowSelectionUI")
        
        # Display data selected (kept here for troubleshooting, handy to have if need to actually see values)
        #tags$strong("Data Values:"), # Placeholder
        #htmlOutput("data_values") # Placeholder
        
      ),
      
      mainPanel(
        fluidPage(
          fluidRow(
            column(8, offset=0, style='padding:0px;', wellPanel(
              tags$strong(tags$span(style="color:grey","Interactive 360 degree visualization (click and drag to rotate)")),
              rglwidgetOutput("model3D"),
              style = "background: white"
              )),
            column(4, align='center', fixedPanel(
              img(src = "www/colorbar.png", height=30, width=100, align="center", alt='image failed to load'),
              htmlOutput('colorbartext'),
              htmlOutput("units"),
              style = "background: white"
            ))
          ),
          fluidRow(
            column(4, offset=0, style='padding:0px;', align='center', wellPanel(
              # Display summary plot centroid
              tags$strong(tags$span(style="color:grey","Relationship with tumor centroid")), 
              plotOutput('centroidPlot', height="150pt", width="130pt"),
              style = "background: white"
              )),
            column(4, offset=0, style='padding:0px;', align='center', wellPanel(
              # Display summary plot periphery
              tags$strong(tags$span(style="color:grey","Relationship with tumor periphery")), 
              plotOutput('peripheryPlot', height="150pt", width="130pt"),
              style = "background: white"
            )),
            column(4, offset=0, style='padding:0px;', align='center', wellPanel(
              # Display summary plot ventricles
              tags$strong(tags$span(style="color:grey","Relationship with brain center")),
              plotOutput('VRPlot', height="150pt", width="130pt"),
              style = "background: white"
            ))
            )
          )
        )
      ),
    #options(shiny.sanitize.errors = TRUE),
    #tags$head(tags$style(type="text/css",".shiny-output-error{visibility: hidden; }")),
    #tags$head(tags$style(".shiny-output-error:before{content: 'Loading data...';visibility: visible; }"))
    )
    invisible(dataTab)
}