inst/shiny/PathoStat/ui/ui_03_ra.R

In mani2012/PathoStat: PathoStat Statistical Microbiome Analysis Package

sam.name <- rownames(as.data.frame(pstat@sam_data))

tabPanel("Visualization",
  tabsetPanel(
    tabPanel("Stacked Barplots",
      tags$br(),
      sidebarLayout(
        sidebarPanel(
          # Sort the samples by a condition
          conditionalPanel(
            condition = "input.group_samples == false",
            selectizeInput('sra_select_conditions', 'Color Samples by Condition', choices=covariates, multiple=TRUE)
          ),
          conditionalPanel(
            condition = "input.group_samples == true",
            selectizeInput('gra_select_conditions', 'Color Samples by Condition', choices=c("All", covariates))
          ),

          # Sample aggregation
          checkboxInput("group_samples", "Group Samples by Condition"),

          # Select taxon level
          selectInput("sra_taxlev", "Tax Level", choices=tax.name, selected="family"),

          # Dynamically generate based on tax level
          uiOutput("sra_order_organisms"),

          # Sort the bars
          radioButtons("sra_sort_by", "Sort By",
          c("No Sorting" = "nosort", "Conditions" = "conditions", "Organisms" = "organisms"), selected="nosort"),

          # Isolate Samples
          selectizeInput('sra_isolate_samples', 'Isolate Samples', choices=sam.name, multiple=TRUE),

          # Legend toggle
          checkboxInput("sra_show_legend", "Show Legend", value=TRUE),

          sliderInput("plot_sra_height", "Plot Height", 600, 1000, value=600, step=50, post="px"),

          actionButton("plot_sra", "Plot"),
          width=3
        ),
        mainPanel(
          uiOutput("dynamic_ra_plot"),
          width=9        
        )
      )
    ),
    tabPanel("Heatmap",
      tags$br(),
      sidebarLayout(
        sidebarPanel(
          # Sort the samples by a condition
          selectizeInput('hmra_select_conditions', 'Color Samples by Condition', choices=covariates, multiple=TRUE),

          # Select taxon level
          selectInput("hmra_taxlev", "Tax Level", choices=tax.name, selected="family"),

          # Dynamically generate based on tax level
          uiOutput("hmra_isolate_organisms"),

          # Sort the bars
          radioButtons("hmra_sort_by", "Sort By",
          c("No Sorting" = "nosort", "Conditions" = "conditions", "Organisms" = "organisms"), selected="nosort"),

          # Isolate Samples
          selectizeInput('hmra_isolate_samples', 'Isolate Samples', choices=sam.name, multiple=TRUE),

          # Legend toggle
          checkboxInput("hmra_logcpm", "log(CPM)", value=FALSE),

          sliderInput("plot_hmra_height", "Plot Height", 600, 1000, value=600, step=50, post="px"),

          actionButton("plot_hmra", "Plot"),
          width=3
        ),
        mainPanel(
          uiOutput("dynamic_hmra_plot"),
          width=9        
        )
      )
    ),
    tabPanel("Boxplots",
      tags$br(),
      sidebarLayout(
        sidebarPanel(
          br(),
          selectizeInput('taxl_single_species', 'Taxonomy Level', choices = tax.name, selected='no rank'),
          selectInput("select_single_species_condition", "Select condition", covariates.colorbar),
          selectInput("ssv_format", "Select data format", c("read count", "relative abundance", "log10 CPM")),
          uiOutput("single_species_ui"),
          actionButton("boxplotButton", "Plot"),
          width=3
        ),
        mainPanel(
          plotlyOutput("single_species_boxplot", width="800px"),
          width=9        
        )
      )
    )
  )
)