inst/shiny/ui_musica.R

In campbio/musicatk: Mutational Signature Comprehensive Analysis Toolkit

shiny_panel_musica <- fluidPage(
 fluidRow(
   tags$head(
     tags$link(rel = "stylesheet", type = "text/css", href = "https://use.fontawesome.com/releases/v5.15.4/css/all.css"),
     tags$script(HTML('
            $(document).ready(function(){
             $("[data-toggle=\'popover\']").popover();
            });
             '))
   ),   
   div(style = "position: relative;",
       box(uiOutput("genome_list"),
    textOutput("genome_select"),
    tags$a(href = "#", 
           tags$i(class = "fas fa-question-circle"),
           title = "Need help?", 
           `data-toggle` = "popover", 
           `data-trigger` = "focus", 
           `data-content` = "The reference genome can be selected from the drop down menu labeled “Choose Genome” that matches the genome build of the variants 
           and the ‘Create Musica Object’ button can then be clicked. Once it’s done, a completion notification message at the bottom right and a variant summary 
           table will appear. The musica object can be downloaded by clicking the ‘Download Musica Object’ button and re-uploaded to save time in subsequent sessions.",
           `data-html` = "true",
           `data-placement` = "left",
           style = "position: absolute; top: 5px; right: 5px; cursor: pointer;"),    
    column(width = 12,
           h3("Settings"),
           #Adding checkbox input ui
           checkboxInput("ref_chr", "Check Reference Chromosomes", TRUE),
           checkboxInput("ref_bases", "Check Reference Bases", TRUE),
           checkboxInput("convert_dbs", "Convert DBS", TRUE),
           checkboxInput("stand_indels", "Standardize Indels", TRUE),
           actionButton("get_musica_object", "Create Musica Object"),
           #Adding download button
           downloadButton("download_musica_object", "Download Musica Object"),
           hr(),
           div(textOutput("musica_contents_summary")),
           hr(),
           div(DT::DTOutput("musica_contents_table"),
           style = "height:500px; overflow-y: scroll;overflow-x: scroll;"),
           hr(),
           #Adding help tooltips
           bsTooltip("genome_list",
                     "Full genome build versions of different organisms",
                     placement = "bottom", trigger = "hover",
                     options = NULL),
           bsTooltip("ref_chr",
                     "Perform a check to ensure
                     that the chromosomes in the variant
                     object match the reference
                     chromosomes in the genome object.",
                     placement = "bottom", trigger = "hover",
                     options = NULL),
           bsTooltip("ref_bases",
                     "Check if the reference bases in the variant object
                     match the reference bases in the genome object.",
                     placement = "bottom", trigger = "hover",
                     options = NULL),
           bsTooltip("convert_dbs",
                     "Convert adjacent SBS into DBS (original SBS are removed)",
                     placement = "bottom", trigger = "hover",
                     options = NULL),
           bsTooltip("stand_indels",
                     "Convert indel style (e.g. 'C > CAT' becomes
                     '- > AT' and 'GCACA > G' becomes 'CACA > -')",
                     placement = "bottom", trigger = "hover",
                     options = NULL),
           bsTooltip("get_musica_object",
                     "Press button to create your musica object.",
                     placement = "bottom", trigger = "hover",
                     options = NULL),
           bsTooltip("download_musica",
                     "Press button to dwownload the musica variants.",
                     placement = "bottom", trigger = "hover",
                     options = NULL)
           ))))
    )