R/outputs_general.R

In csoneson/iSEE: Interactive SummarizedExperiment Explorer

#' Render general output for the app
#'
#' Create rendering expressions for \code{\link{iSEE}} outputs that are general to the entire app, not just specific panels.
#'
#' @param se A \linkS4class{SummarizedExperiment} object containing the data of interest.
#' @param input The Shiny input object from the server function.
#' @param output The Shiny output object from the server function.
#' @param session The Shiny session object from the server function.
#' @param pObjects An environment containing global parameters generated in the \code{\link{iSEE}} app.
#' @param rObjects A reactive list of values generated in the \code{\link{iSEE}} app.
#'
#' @return A \linkS4class{NULL} is invisibly returned
#' and rendering expressions for general app features are added to \code{output}.
#'
#' @author Aaron Lun, Kevin Rue-Albrecht
#'
#' @rdname INTERNAL_create_general_output
#' @importFrom utils zip
#' @importFrom shiny downloadHandler renderPlot checkboxGroupInput actionButton downloadButton withProgress incProgress
#' @importFrom listviewer jsonedit renderJsonedit
#' @importFrom S4Vectors metadata
.create_general_output <- function(se, input, output, session, pObjects, rObjects) {
    # nocov start
    output[[.generalLinkGraphPlot]] <- renderPlot({
        force(input[[.generalLinkGraph]]) # trigger re-rendering every time the button is clicked.
        .snapshot_graph_linkedpanels(pObjects$selection_links,
            vapply(pObjects$memory, .getPanelColor, ""))
    })
    # nocov end
    # nocov start
    output[[.generalExportOutputUI]] <- renderUI({
        force(input[[.generalExportOutput]]) # trigger rerendering every time the button is clicked.
        all_options <- .define_export_choices(pObjects$memory)
        tagList(
            checkboxGroupInput(.generalExportOutputChoices, label=NULL,
                choices=all_options, selected=all_options),
            actionButton(.generalExportOutputAll, label="Select all"),
            actionButton(.generalExportOutputNone, label="Select none"),
            downloadButton(.generalExportOutputDownload, "Download")
        )
    })
    # nocov end

    # nocov start
    output[[.generalMemoryExport]] <- downloadHandler(
        filename="iSEE_memory.rds",
        content=function(file) {
            vals <- .gather_current_memory(se, input, pObjects)
            saveRDS(file=file, vals)
        }
    )
    # nocov end

    # nocov start
    output[[.generalExportOutputDownload]] <- downloadHandler(
        filename="iSEE_exports.zip",
        content=function(file) {
            dumptmp <- tempfile()
            dir.create(dumptmp)
            oldwd <- getwd()
            setwd(dumptmp)

            on.exit({
                setwd(oldwd)
                unlink(dumptmp, recursive=TRUE)
            })

            # Loops through all panels, asks them for how they wish
            # to be summarized, and then saves their gunk to file.
            all.files <- list()
            n_plots <- length(input[[.generalExportOutputChoices]])
            withProgress(message = 'Generating plots', value = 0, max = n_plots, {
                for (i in input[[.generalExportOutputChoices]]) {
                    i_object <- pObjects$memory[[i]]
                    incProgress(1, detail = sprintf("Making '%s'", .getFullName(i_object)))
                    
                    all.files[[i]] <- .exportOutput(i_object, se=se,
                        all_memory=pObjects$memory, all_contents=pObjects$contents)
                }
                
            }, session = session)

            zip(file, files=unlist(all.files))
        }
    )
    # nocov end
    
    # nocov start
    output[["mdd"]] <- listviewer::renderJsonedit({
      mdd <- metadata(se)
      jsonedit(mdd)
    })
    # nocov end
    
    invisible(NULL)
}

#' Define export choices
#'
#' Define the available panels that can be chosen for exporting content.
#'
#' @param all_memory A list of \linkS4class{Panel}s specifying the current state of the app.
#'
#' @return A character vector of length equal to \code{all_memory}, containing the encoded panel names.
#' The names of this vector are set to the full panel names for display purposes.
#'
#' @author Aaron Lun
#'
#' @rdname INTERNAL_define_export_choices
.define_export_choices <- function(all_memory) {
    if (length(all_memory)) {
        all_options <- vapply(all_memory, .getEncodedName, "")
        names(all_options) <- vapply(all_memory, .getFullName, "")
    } else {
        all_options <- character(0)
    }
    all_options
}