R/dash_DE_ui.R

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

ui_DE <- function(id) {
    ns <- NS(id)
    DE_opts <- c()
    if(.check_package_installed("limma", "3.44.0", "silent")) {
        DE_opts <- "limma"
    }
    if(.check_package_installed("DoubleExpSeq", "1.1", "silent")) {
        DE_opts <- c(DE_opts, "DoubleExpSeq")
    }
    if(.check_package_installed("edgeR", "3.32.0", "silent")) {
        DE_opts <- c(DE_opts, "edgeR")
    }
    if(.check_package_installed("DESeq2", "1.30.0", "silent")) {
        DE_opts <- c(DE_opts, "DESeq2")
    }
    # if(.check_package_installed("satuRn", "1.4.2", "silent")) {
        # DE_opts <- c(DE_opts, "satuRn")
    # }
    if(is.null(DE_opts)) {
        DE_opts <- "(none) - please install limma, DESeq2, edgeR, DoubleExpSeq"
    }
    fluidRow(
        .ui_notice(),
        column(4,
            selectInput(ns('method_DE'), 'Method', 
                DE_opts),
            selectInput(ns('variable_DE'), 'Variable', 
                c("(none)")),
            selectInput(ns('nom_DE'), 'Nominator', 
                c("(none)")),
            selectInput(ns('denom_DE'), 'Denominator', 
                c("(none)")),
            selectInput(ns('batch1_DE'), 'Batch Factor 1', 
                c("(none)")),
            selectInput(ns('batch2_DE'), 'Batch Factor 2', 
                c("(none)")),
            conditionalPanel(ns = ns,
                condition = "['(time series)'].indexOf(input.nom_DE) >= 0",
                numericInput(ns("degrees_DE"), 
                    label = "Splines degrees of freedom (limma only)", 
                    value = 1, min = 1, max = 5)
            ),
            shinyWidgets::prettyRadioButtons(
                inputId = ns("de_IRmode"),
                label = "Intron Retention analysis (mode):", 
                choiceNames = c(
                    "All Introns (IR-Ratio)", 
                    "Annotated IR events (IR-Ratio)", 
                    "Annotated IR events (binary PSI)"
                ), 
                choiceValues = c("all", "annotated", "annotated_binary"),
            ),
            shinyWidgets::materialSwitch(
               inputId = ns("adjP_DE"),
               label = "Sort by Adjusted P Values", right = TRUE,
               value = TRUE, status = "success"
            ),
            # actionButton(ns("perform_DE"), "Perform DE"),
            # shinyFilesButton(ns("load_DE"), label = "Load DE", 
                    # title = "Load DE from RDS", multiple = FALSE),
            # shinySaveButton(ns("save_DE"), "Save DE", "Save DE as...", 
                # filetype = list(RDS = "Rds")),
            actionBttn(ns("perform_DE"), "Perform DE",
                style = "gradient", color = "success"), br(), br(),
            textOutput(ns("warning_DE")), br(),
            wellPanel(style = "max-width: 300px",
                shinySaveAttnButton(ns("save_DE"), 
                    label = "Save Analysis to file", 
                    title = "Save Analysis to RDS", 
                    filetype = list(RDS = "Rds")), br(), br(),
                shinyFilesAttnButton(ns("load_DE"), 
                    label = "Load Analysis from file", 
                    title = "Load Analysis from RDS", multiple = FALSE)            
            )
        ),
        column(8,
            actionButton(ns("clear_selected_DE"), "Clear Selected Events"), 
            br(), br(),
            div(style = 'overflow-x: scroll',  
                DT::dataTableOutput(ns('DT_DE'))
            )
        )
    )
}