R/ui.R

In Hla-Lab/SeuratExplorer: An Interactive Shiny App for Visualizing scRNAseq Data Processed in Seurat

# ui.R
# R shiny UI for SeuratExplorer

#' UI for shiny App interface
#' @import Seurat ggplot2
#' @import dplyr scales shiny shinydashboard
#' @import stringr
ui = function(){
  ex_genes = "Actb, Tubb1, S1pr1..."
  
  # Header ----
  header = dashboardHeader(title = "SeuratExplorer")
  
  # Sidebar ----
  sidebar = dashboardSidebar(
    sidebarMenu(
      menuItem(text = "Dataset",
               tabName = "dataset",
               icon=icon("database")
               )
      ),
    conditionalPanel(
      condition = "output.file_loaded",                                         
      selectInput("annotation",
                  label = "Annotation:",
                  choices = NULL),
      textOutput("annotation_identities")
    ),
    sidebarMenu(
      menuItem(text = "UMAP",
               tabName = "umap",
               icon=icon(name="cloudsmith")),
      menuItem("Violin",
               tabName = "vln",
               icon=icon("hourglass")),
      menuItem("DotPlot",
               tabName = 'dot',
               icon=icon("braille")),
      menuItem("Differential Expression",
               tabName = 'de',
               icon=icon("list")),
      menuItem("Ligand-Receptor",
               tabName = 'lr',
               icon=icon("connectdevelop")),
      menuItem("Developer Testing",
               tabName = 'dev',
               icon=icon("braille"))
    )
  )
  
  # BODY ----
  tab_list = list()
  
  tab_list[["dataset"]] = tabItem("dataset",
            box(fileInput("dataset_file", "Choose Seurat .rds file:", accept = '.rds'), width = 4),
            dataTableOutput("dataset_meta")
            )
  
  tab_list[["umap"]] = tabItem("umap",
            sidebarLayout(position = "left", fluid = TRUE,
              mainPanel(
                plotOutput("umap"),
                plotOutput("featureplot"),
                width = 8
              ),
              sidebarPanel(
                selectInput("umap_splitby", label = "Split by:", choices = NULL),
                textInput("umap_gene", "Feature(s):", placeholder = ex_genes, value = NULL),
                width = 4
              )
            )
          )
  
  
  tab_list[["vln"]] = tabItem("vln",
            sidebarLayout(position = "left", fluid = TRUE,
              mainPanel(plotOutput("vln")),
              sidebarPanel(
                textInput("vln_gene", label = "Feature(s):", placeholder = ex_genes, value = NULL),
                selectInput("vln_splitby", label = "Split by:", choices = NULL),
                selectInput("vln_idents", label = "Identities:", choices = NULL, multiple = TRUE)
                )
              )
            )
  
  tab_list[["dot"]] = tabItem("dot",
            sidebarLayout(position = "left", fluid = TRUE,
              mainPanel(plotOutput("dot")),
              sidebarPanel(
                textInput("dot_gene", "Feature(s):", placeholder = ex_genes, value = NULL),
                selectInput("dot_idents", label = "Identities:", choices = NULL, multiple = TRUE)
              )
            )
          )
  
  tab_list[["de"]] = tabItem("de",
            box(textOutput("de_warning"), title = "WARNING", background = "red", width = 12),
            box(
              selectInput("de_ident", label = "Identity:", choices = NULL, multiple = FALSE),
              selectInput("de_variable", label = "Variable:", choices = NULL),
              selectInput("de_reference", label = "Reference condition:", choices = NULL),
              selectInput("de_experimental", label = "Experimental condition:", choices = NULL)
            ),
            box(
              actionButton("de_analyze", "Analyze"),
              width = 6),
            dataTableOutput("de_table"),
            conditionalPanel(
              condition = "output.de_loaded",
              downloadButton("de_download", "Download"),
              width = 4
              )
            )
  
  tab_list[["lr"]] = tabItem("lr",
            box(
              textOutput("lr_warning"), title = "WARNING", background = "red", width = 12),
            box(
              selectInput("lr_db", label = "Database:", choices = NULL, multiple = FALSE),
              selectInput("lr_idents", label = "Idents:", choices = NULL, multiple = TRUE),
              selectInput("lr_condition", label = "Condition (Optional):", choices = NULL, multiple = FALSE),
              conditionalPanel(
                condition = "input.lr_condition != 'None'",
                selectInput("lr_reference", label = "Reference condition:", choices = NULL),
                selectInput("lr_experimental", label = "Experimental condition:", choices = NULL)
              )
            ),
            box(  
              sliderInput("lr_signature_cutoff", label = "Signature Padj Cutoff:", min = 0.01, max = 0.15, value = 0.05, step = 0.01),
              sliderInput("lr_deg_cutoff", label = "DEG Padj Cutoff:", min = 0.01, max = 0.15, value = 0.05, step = 0.01),
            ),
            box(
              actionButton("lr_analyze", "Analyze"),
              width = 4),
            dataTableOutput("lr_table"),
            conditionalPanel(
              condition = "output.lr_loaded",
              downloadButton("lr_download", "Download"),
              width = 4
            )
          )
  
  tab_list[["dev"]] = tabItem("dev",
            textInput(inputId = "test", label = "Input"),
            textOutput("dev_out")
            )
  
  body = dashboardBody(
    div(class= "tab-content", tab_list)
    )
  
  ui_out = dashboardPage(header, sidebar, body)
  return(ui_out)
}