inst/shinyapp/ui.R

In rnabioco/clustifyr: Classifier for Single-cell RNA-seq Using Cell Clusters

# Define UI for data upload app ----
ui <- dashboardPage(
  title = "clustifyr app",
  skin = "green",
  dashboardHeader(
    title = div(
      tags$a(
        href = 'https://github.com/rnabioco/clustifyr',
        tags$img(src = 'logo.png', width = "18%")
      ),
      "clustifyr Shiny app"
    )
  ),
  dashboardSidebar(
    # tags$img(
    #   src = 'logo.png',
    #   width = "1000%",
    #   style = 'position: fixed; bottom: 0;right: 0;'
    # ),
    sidebarMenu(
      id = "tabs",
      menuItem("Dashboard", tabName = "dashboard", icon = icon("dashboard")),
      menuItem("Load Matrix", tabName = "matrixLoad", icon = icon("th")),
      menuItem("Load Metadata", tabName = "metadataLoad", icon = icon("list")),
      menuItem(
        "Load Reference",
        tabName = "clusterRef",
        icon = icon("database")
      ),
      menuItem(
        "Cell type inference",
        tabName = "clustifyres",
        icon = icon("calculator")
      ),
      menuItem("", tabName = "blank"),
      menuItem("Explore GEO", tabName = "someta", icon = icon("hdd"))
    )
  ),
  dashboardBody(
    shinyDashboardThemes(theme = "poor_mans_flatly"),
    tabItems(
      tabItem(
        tabName = "dashboard",
        # js stuff ----
        useShinyjs(),
        use_bs_tooltip(),
        tags$head(
          tags$script(HTML(js2))
        ),
        tags$head(tags$style(HTML(
          '
            .skin-green .sidebar .inactiveLink {
                color: black;
                opacity : 25%;
            }'
        ))),
        tags$head(tags$style(
          ".inactiveLink {
                           pointer-events: none;
                           cursor: not-allowed;
                           }"
        )),
        tags$head(tags$style(HTML(
          '
            .skin-green .sidebar .doneLink {
                color: green;
            }'
        ))),
        tags$head(tags$style(HTML(
          '
            .skin-green .sidebar .doneLink.active > a {
                color: green;
                border-left-color: green;
            }'
        ))),
        tags$head(tags$style(HTML(
          '
            .skin-green .sidebar .doneLink:hover {
                color: green;
                border-left-color: green;
            }'
        ))),

        # waiter stuff ----
        use_waiter(),

        # load example data ----
        actionButton(
          "example",
          "Load example data",
          icon = icon("space-shuttle")
        ) %>%
          bs_embed_tooltip(
            "Use example data from GSE113049 for walkthrough",
            placement = "right"
          ),

        # Horizontal line ----
        tags$hr(),

        # readme
        includeMarkdown("README.md"),

        # Input: Checkbox if file has header ----
        checkboxInput("header", "Header", TRUE),

        # Horizontal line ----
        tags$hr(),

        # Input: Select separator ----
        radioButtons(
          "sepMat",
          "Separator - Matrix",
          choices = c(
            Comma = ",",
            Semicolon = ";",
            Tab = "\t"
          ),
          selected = ","
        ),

        radioButtons(
          "sepMeta",
          "Separator - Metadata",
          choices = c(
            Comma = ",",
            Semicolon = ";",
            Tab = "\t"
          ),
          selected = ","
        ),

        # Input: Select number of rows to display ----
        radioButtons(
          "dispMat",
          "Display - Matrix",
          choices = c(
            Head = "head",
            All = "all"
          ),
          selected = "head"
        ),
        radioButtons(
          "dispMeta",
          "Display - Metadata",
          choices = c(
            Head = "head",
            All = "all"
          ),
          selected = "head"
        )
      ),
      tabItem(
        tabName = "matrixLoad",
        h2("Load Counts (raw or normalized) Matrix"),
        # Input: Select a file ----
        fileInput(
          "file1",
          "Choose Matrix File",
          multiple = TRUE,
          accept = c(
            "text/csv",
            "text/comma-separated-values,text/plain",
            ".csv",
            ".xlsx",
            ".tsv",
            ".rds",
            ".rda",
            ".rdata",
            ".gz"
          )
        ) %>%
          bs_embed_tooltip(
            "Accepted file types: plain or gz text files, and rds/rda/rdata for Seurat/SCE",
            placement = "right"
          ),

        # GEO id load ----
        actionButton("geo1", "or from GEO id", icon = icon("search")) %>%
          bs_embed_tooltip(
            "Alternatively, load data directly from GEO with ID",
            placement = "right"
          ),

        actionButton("matrixPopup", "Display UMI Matrix in popup"),
        tags$hr(),
        DTOutput("contents1"), # UMI Count Matrix
        tags$hr()
      ),
      tabItem(
        tabName = "metadataLoad",
        h2("Load Metadata"),
        fileInput(
          "file2",
          "Choose Metadata File",
          multiple = FALSE,
          accept = c(
            "text/csv",
            "text/comma-separated-values,text/plain",
            ".csv",
            ".xlsx",
            ".tsv",
            ".rds",
            ".rda",
            ".rdata",
            ".gz"
          )
        ) %>%
          bs_embed_tooltip(
            "Accepted file types: plain or gz text files, and rds/rda/rdata for Seurat/SCE",
            placement = "right"
          ),

        # GEO id load ----
        actionButton("geo2", "or from GEO id", icon = icon("search")) %>%
          bs_embed_tooltip(
            "Alternatively, load data directly from GEO with ID",
            placement = "right"
          ),

        actionButton("metadataPopup", "Display Metadata table in popup"),
        h2("Choose column in metadata with cluster info"),
        selectInput("metadataCellType", NULL, choice = list("")) %>%
          bs_embed_tooltip(
            "Select from dropdown, or click on preview column below",
            placement = "right"
          ),
        tags$hr(),
        DTOutput('contents2'),
        #DT::dataTableOutput("contents2"), # Metadata table
        tags$hr(),
        uiOutput("colclicked")
      ),
      tabItem(
        tabName = "clusterRef",
        h2(
          "Choose built-in reference dataset or upload average expression matrix"
        ),
        selectInput(
          "dataHubReference",
          "ClustifyrDataHub Reference:",
          choices = list(
            "ref_MCA",
            "ref_tabula_muris_drop",
            "ref_tabula_muris_facs",
            "ref_mouse.rnaseq",
            "ref_moca_main",
            "ref_immgen",
            "ref_hema_microarray",
            "ref_cortex_dev",
            "ref_pan_indrop",
            "ref_pan_smartseq2",
            "ref_mouse_atlas"
          )
        ) %>%
          bs_embed_tooltip(
            "Select from pre-built references in clustifyrdatahub",
            placement = "right"
          ),
        actionButton(
          "ref_linkgo",
          label = "Go to original source",
          icon = icon("link")
        ) %>%
          bs_embed_tooltip(
            "For more info on the reference datasets",
            placement = "right"
          ),
        tags$hr(),
        h2("Or load reference table"),
        fileInput(
          "file3",
          "Choose Reference Average Expression File",
          multiple = FALSE,
          accept = c(
            "text/csv",
            "text/comma-separated-values,text/plain",
            ".csv",
            ".tsv",
            ".xlsx",
            ".gz"
          )
        ) %>%
          bs_embed_tooltip(
            "Alternatively, choose local file of average gene expression by cell type",
            placement = "right"
          ),
        tags$hr(),
        uiOutput("ref_summary"),
        DTOutput("contents3", height = "300px"),
        tags$hr()
      ),
      tabItem(
        tabName = "clustifyres",
        box(
          id = "box_clustifym",
          collapsible = TRUE,
          collapsed = TRUE,
          solidHeader = TRUE,
          status = "info",
          title = "clustifyr messages",
          htmlOutput("clustifym")
        ) %>%
          bs_embed_tooltip("Console messages from run", "right"),
        div(
          style = "display:inline-block",
          downloadButton(
            "downloadReference",
            "Download average expression matrix"
          ) %>%
            bs_embed_tooltip(
              "Note: this is the same file needed to use the current dataset as reference in the future",
              "bottom"
            ),
          downloadButton(
            "downloadClustify",
            "Download clustify results matrices"
          ) %>%
            bs_embed_tooltip(
              "Cell type inference as sheet1, correlation matrix as sheet2, of xlsx",
              "bottom"
            )
        ),
        tags$hr(),
        # actionButton("uploadClustify", "Upload reference matrix"),
        h2("Average Expression Matrix"),
        DT::dataTableOutput("reference", height = "300px"), # Reference Matrix
        tags$hr(),
        h2("Ranked Correlation Matrix"),
        DT::dataTableOutput("clustify", height = "300px"), # Clustify Matrix
        tags$hr(),
        h2("Cell Type Inference Results"),
        DT::dataTableOutput("corToCall", height = "300px"),
        tags$hr(),
        plotOutput("hmap", height = "900px"),
        tags$hr(),
      ),
      tabItem(
        tabName = "someta",
        h2(
          "GEO scRNA-seq records, hover to see truncated text, click to preview files"
        ),
        DT::dataTableOutput("someta", height = "1000px")
      )
    )
  )
)