inst/shiny/v1.3/gene_expression/UI_projection.R

In romanhaa/cerebroApp: Interactive visualization of scRNA-seq data with Cerebro

##----------------------------------------------------------------------------##
## UI element with layout for user input and plot.
##----------------------------------------------------------------------------##
output[["expression_projection_UI"]] <- renderUI({
  fluidRow(
    column(
      width = 3, offset = 0, style = "padding: 0px;",
      tagList(
        cerebroBox(
          title = tagList(
            "Main parameters",
            actionButton(
              inputId = "expression_projection_main_parameters_info",
              label = "info",
              icon = NULL,
              class = "btn-xs",
              title = "Show additional information for this panel.",
              style = "margin-left: 5px"
            )
          ),
          tagList(
            shinyWidgets::radioGroupButtons(
               inputId = "expression_analysis_mode",
               label = NULL,
               choices = c("Gene(s)", "Gene set"),
               status = "primary",
               justified = TRUE,
               width = "100%"
            ),
            uiOutput("expression_projection_input_type_UI"),
            uiOutput("expression_projection_select_projection_UI")
          )
        ),
        cerebroBox(
          title = tagList(
            "Additional parameters",
            actionButton(
              inputId = "expression_projection_additional_parameters_info",
              label = "info",
              icon = NULL,
              class = "btn-xs",
              title = "Show additional information for this panel.",
              style = "margin-left: 5px"
            )
          ),
          uiOutput("expression_projection_additional_parameters_UI"),
          collapsed = TRUE
        ),
        cerebroBox(
          title = tagList(
            "Group filters",
            actionButton(
              inputId = "expression_projection_group_filters_info",
              label = "info",
              icon = NULL,
              class = "btn-xs",
              title = "Show additional information for this panel.",
              style = "margin-left: 5px"
            )
          ),
          uiOutput("expression_projection_group_filters_UI"),
          collapsed = TRUE
        ),
        cerebroBox(
          title = tagList(
            "Color scale",
            actionButton(
              inputId = "expression_projection_color_scale_info",
              label = "info",
              icon = NULL,
              class = "btn-xs",
              title = "Show additional information for this panel.",
              style = "margin-left: 5px"
            )
          ),
          tagList(
            uiOutput("expression_projection_color_scale_UI"),
            uiOutput("expression_projection_color_range_UI"),
          ),
          collapsed = TRUE
        )
      )
    ),
    column(
      width = 9, offset = 0, style = "padding: 0px;",
      cerebroBox(
        title = tagList(
          boxTitle("Dimensional reduction"),
          tagList(
            actionButton(
              inputId = "expression_projection_info",
              label = "info",
              icon = NULL,
              class = "btn-xs",
              title = "Show additional information for this panel.",
              style = "margin-right: 3px"
            ),
            shinyFiles::shinySaveButton(
              "expression_projection_export",
              label = "export to PDF",
              title = "Export dimensional reduction to PDF file.",
              filetype = "pdf",
              viewtype = "icon",
              class = "btn-xs",
              style = "margin-right: 3px"
            ),
            shinyWidgets::dropdownButton(
              tags$div(
                tags$style(
                  HTML("div.awesome-checkbox {margin-top: 10px;}")
                ),
                style = "color: black !important;",
                tagList(
                  uiOutput("expression_projection_point_border_UI"),
                  uiOutput("expression_projection_genes_in_separate_panels_UI"),
                  uiOutput("expression_projection_scales_UI")
                )
              ),
              circle = FALSE,
              icon = icon("cog"),
              inline = TRUE,
              size = "xs"
            )
          )
        ),
        tagList(
          shinycssloaders::withSpinner(
            plotly::plotlyOutput(
              "expression_projection",
              width = "auto",
              height = "85vh"
            ),
            type = 8,
            hide.ui = FALSE
          ),
          tags$br(),
          htmlOutput("expression_number_of_selected_cells"),
          tags$br(),
          htmlOutput("expression_genes_displayed")
        )
      )
    )
  )
})

##----------------------------------------------------------------------------##
## Info box that gets shown when pressing the "info" button.
##----------------------------------------------------------------------------##
observeEvent(input[["expression_projection_main_parameters_info"]], {
  showModal(
    modalDialog(
      expression_projection_main_parameters_info$text,
      title = expression_projection_main_parameters_info$title,
      easyClose = TRUE,
      footer = NULL,
      size = "l"
    )
  )
})

##----------------------------------------------------------------------------##
## Text in info box.
##----------------------------------------------------------------------------##
expression_projection_main_parameters_info <- list(
  title = "Main parameters for gene (set) expression",
  text = HTML("
    The elements in this panel allow you to control what and how results are displayed across the whole tab.
    <ul>
      <li><b>Gene(s) / Gene set:</b> Select whether you would like to select individual genes or gene sets. In the case of 'Gene(s)', you can select one or multiple genes from the input field below. If you select multiple genes, the mean expression across the selected genes will be calculated for each cell. If you select 'Gene set', you can select a gene set from the MSigDB. Species-specific gene names will be tried to retrieve, otherwise gene name matching is attempted. A list of which genes are present or missing in the data set can be found below the projection.</li>
      <li><b>Projection:</b> Select here which projection you want to see in the scatter plot on the right.</li>
    </ul>
    "
  )
)