inst/shiny/PathoStat/ui/ui_02_filter.R

In mani2012/PathoStat: PathoStat Statistical Microbiome Analysis Package

tabPanel("Summary and Filter",
  tabsetPanel(
    tabPanel("Filtering",
      br(),
      sidebarLayout(
        sidebarPanel(
          br(),
          selectInput("filter_type", "Select filter type", c("By Metadata", "By Samples", "By Microbes")),

          # Filtering by metadata
          conditionalPanel(condition = "input.filter_type == 'By Metadata'",
            selectInput("select_condition_sample_filter_sidebar", "Select a variable", c("Reads", covariates)),
            conditionalPanel(condition = "output.filter_type == 'num.continuous'",
              helpText("Please select range of the feature to keep"),
              numericInput("num_filter_min", "Min", 0),
              numericInput("num_filter_max", "Max", 0),
              withBusyIndicatorUI(
                actionButton("filter_num", "Filter")
              )
            ),
            conditionalPanel(condition = "output.filter_type == 'cat'",
              helpText("Please select levels of the feature to keep"),
              uiOutput("filter_cat_options"),
              withBusyIndicatorUI(
                actionButton("filter_cat", "Filter")
              )
            )
          ),
          
          # Filtering by sample
          conditionalPanel(condition = "input.filter_type == 'By Samples'",
            selectizeInput('filterSample', 'Choose sample name(s) for removal', 
                           choices = sample.names.all, selected=NULL, multiple = TRUE),
            withBusyIndicatorUI(
              actionButton("filterSampleButton", "Filter")
            )
          ),

          # Filtering by microbes
          conditionalPanel(condition = "input.filter_type == 'By Microbes'",
            br(),
            selectInput("filter_type_micro", "Select filter type",
                 c("By mapped read number",
                   "By relative abundace",
                   "By prevalence")
            ),
            conditionalPanel(condition = "input.filter_type_micro == 'By mapped read number'",
              helpText("Please select the average minimum read mapped"),
              numericInput("read_filter_min_micro", "Min", 0, min = 0, max = 10000),
              withBusyIndicatorUI(
                actionButton("filter_read_micro", "Filter")
              )
            ),
            conditionalPanel(condition = "input.filter_type_micro == 'By relative abundace'",
              helpText("Please select average minimum RA"),
              numericInput("ra_filter_min_micro", "Min", 0, min = 0, max = 1),
              withBusyIndicatorUI(
                actionButton("filter_ra_micro", "Filter")
              )
            ),
            conditionalPanel(condition = "input.filter_type_micro == 'By prevalence'",
              helpText("Please select minimum prevalence"),
              numericInput("prev_filter_min", "Min", 0, min = 0, max = 1),
              withBusyIndicatorUI(
                actionButton("filter_prev_micro", "Filter")
              )
            )
          ),
          br(),
          withBusyIndicatorUI(
            actionButton("reset_button", "Reset")
          ),
          br(),    
          downloadButton('download_rds', 'Download (.rds)'),
          width=3
        ),
        mainPanel(
          fluidRow(
            column(6,
              h4("Overall Summary Table", align="center"),
              br(),
              tableOutput("contents_summary")
            ),
            column(6,
              h4("Variable Summary Plots", align="center"),
              br(),
              plotlyOutput("summary_plot_top", height="300px"),
              plotlyOutput("summary_plot_bottom", height="300px")
            )
          ), 
          width=9
        )
      )
    ),
    tabPanel("Categorize",
      tags$br(),
      sidebarLayout(
        sidebarPanel(
          selectizeInput('bin_cov', 'Covariate', choices=num_covariates, multiple=FALSE),
          uiOutput("nbins"),
          textInput('bin_breaks', 'Custom Breaks (Comma Delimited)'),
          verbatimTextOutput("bin_to1"),
          textInput('bin_labels', 'Custom Labels (Comma Delimited)'),
          verbatimTextOutput("bin_to2"),
          textInput("new_covariate", "Covariate Label", value = "new_cov"),
          actionButton("create_bins", "Create Bins"),
          width=5
        ),
        mainPanel(
          plotlyOutput("unbin_plot", height="200px"),
          br(),
          plotlyOutput("bin_plot"),
          width=7
        )
      )
    ),    
    tabPanel("Read Counts & Relative Abundance",
      br(),
      sidebarLayout(
        sidebarPanel(
          br(),
          selectizeInput('taxlTable', 'Taxonomy Level', choices = tax.name, selected='no rank'),
          width=3
        ),
        mainPanel(
          tabsetPanel(
            tabPanel("Relative Abundance",
              br(),
              DT::dataTableOutput("TaxRAtable", width='95%'),
              downloadButton('downloadData', 'Download (.csv)')
            ),
            tabPanel("Read Counts",
              br(),
              DT::dataTableOutput("TaxCountTable",width='95%'),
              downloadButton('downloadCountData', 'Download (.csv)')
            )
            #coreOTUModuleUI("coreOTUModule")
          ), 
          width=9
        )
      )
    )
  )
)