R/dash_ref_new_ui.R

In alexchwong/SpliceWiz: interactive analysis and visualization of alternative splicing in R

ui_ref_new <- function(id) {
    ns <- NS(id)
    fluidRow(
        .ui_notice(),
        column(6,
            # h4("Select Reference Directory"),
            wellPanel(
                h4("Create / Select Directory for the Reference"),
                tags$div(title = paste("Choose a directory for SpliceWiz",
                        "to create its reference"),
                    splitLayout(cellWidths = c("30%", "70%"), 
                        shinyDirButton(ns("dir_reference_path"), 
                            label = "Select Reference Directory", 
                            title = "Select Reference Directory",
                            buttonType = "primary"
                        ), textOutput(ns("txt_reference_path"))
                    )
                )
            ), br(),
            wellPanel(
                h4("Source Ensembl Reference"),
                selectInput(ns('release'), 'Select Release', width = '100%',
                    choices = c("")),
                selectInput(ns('species'), 'Select Species', width = '100%',
                    choices = c("")),
                selectInput(ns('fasta'), 'Select Genome', width = '100%',
                    choices = c("")),
                selectInput(ns('gtf'), 'Select Annotation', width = '100%',
                    choices = c(""))
            ),
            wellPanel(
                h4("Source FASTA / GTF Files"),
                tags$div(title = "Choose a user-supplied genome fasta file",
                    splitLayout(cellWidths = c("35%", "65%"), 
                        shinyFilesButton(ns("file_genome"), 
                            label = "Choose genome FASTA File", 
                            title = "Choose genome FASTA File", 
                            buttonType = "primary",
                            multiple = FALSE
                        ),
                        textOutput(ns("txt_genome"))
                    )
                ), br(),
                tags$div(title = paste("Choose a user-supplied transcript",
                    "reference gtf file"),
                    splitLayout(cellWidths = c("35%", "65%"), 
                        shinyFilesButton(ns("file_gtf"), 
                            label = "Choose transcriptome GTF File", 
                            title = "Choose transcriptome GTF File", 
                            buttonType = "primary",
                            multiple = FALSE
                        ),
                        textOutput(ns("txt_gtf"))
                    )
                )
            )
        ),
        column(6,
            wellPanel(
                h4("Additional Files"),
                tags$div(title = "Species for Gene Ontology reference",
                    selectInput(ns('newref_species_GO'),
                        paste('Species (Gene Ontology)'),
                        c("(none)", "Homo sapiens", "Mus musculus")
                    )
                ),
                tags$div(title = paste("SpliceWiz will auto-populate default",
                        "mappability and non-polyA reference files for",
                        "hg38, hg19, mm10 and mm9 genomes"),
                    selectInput(ns('newref_genome_type'),
                        paste('Select Genome Type to set',
                            'Mappability and non-PolyA files'),
                        c("(none)", "hg38", "mm10", "hg19", "mm9")
                    )
                ),
                tags$div(title = paste("Select Mappability Exclusion file.",
                        "This is typically a 3 columns",
                        "of values containing seqnames,",
                        "start and end coordinates of low-mappability regions"),
                    shinyFilesButton(ns("file_mappa"), 
                        label = "Choose Mappability Exclusion file", 
                        title = "Choose Mappability Exclusion file", 
                        buttonType = "primary",
                        multiple = FALSE
                    ),
                    actionButton(ns("clear_mappa"), "Clear",
                        class = "btn-outline-danger"),
                    textOutput(ns("txt_mappa"))
                ), br(),
            
                tags$div(title = paste("Select Non-PolyA reference file.",
                        "This is used by processBAM",
                        "to calculate reads from known non-polyadenylated",
                        "transcripts to assess",
                        "quality of poly-A enrichment in sample QC"),
                    shinyFilesButton(ns("file_NPA"), 
                        label = "Choose non-PolyA BED file", 
                        title = "Choose non-PolyA BED file", 
                        buttonType = "primary",
                        multiple = FALSE),
                    actionButton(ns("clear_NPA"), "Clear",
                        class = "btn-outline-danger"),
                    textOutput(ns("txt_NPA"))
                ), br(),
                tags$div(title = paste("Select Blacklist file.",
                        "This is typically a 3 columns of values",
                        "containing seqnames, start and end coordinates",
                        "of regions to exclude from processBAM analysis"),
                    shinyFilesButton(ns("file_bl"), 
                        label = "Choose blacklist BED file", 
                        title = "Choose blacklist BED file", 
                        buttonType = "primary",
                        multiple = FALSE),
                    actionButton(ns("clear_bl"), "Clear",
                        class = "btn-outline-danger"),
                    textOutput(ns("txt_bl"))
                )
            ),
            wellPanel(
                h4("Load Demo Reference"),
                tags$div(
                    shinyWidgets::actionBttn(ns("load_ref_example"), 
                        "Load Demo FASTA / GTF",
                        style = "gradient", color = "danger"
                    ), br(), br(), textOutput(ns("txt_demo"))
                )
            ),
            wellPanel(
                h4("Start Building Reference"),
                tags$div(
                    shinyWidgets::actionBttn(ns("buildRef"), 
                        "Build Reference", 
                        style = "gradient", color = "primary"),
                    shinyWidgets::actionBttn(ns("clearNewRef"), 
                        "Clear settings", 
                        style = "gradient", color = "warning"),
                )
            ),
            uiOutput(ns("refStatus"))
        )
    )
}