R/app_startup.R

In safetyGraphics: Interactive Graphics for Monitoring Clinical Trial Safety

#' Startup code for shiny app
#' 
#' Prepare inputs for safetyGraphics app - run before app is initialized. 
#' 
#' @param domainData named list of data.frames to be loaded in to the app. Sample AdAM data from the safetyData package used by default
#' @param meta data frame containing the metadata for use in the app. If no metadata is provided (default value is NULL), metatdata is generated by `makeMeta()`. 
#' @param charts list of charts in the format produced by safetyGraphics::makeChartConfig()
#' @param mapping list specifying the initial mapping values for each data mapping for each domain (e.g. list(aes= list(id_col='USUBJID', seq_col='AESEQ')). 
#' @param autoMapping boolean indicating whether the app should attempt to automatically detect data standards and generate mappings for the data provided. Values specified in the `mapping` parameter overwrite automatically generated mappings when both are found. Defaults to true.
#' @param filterDomain domain used for the data/filter tab. Demographics ("`dm`") is used by default. Using a domain that is not one record per participant is not recommended. 
#' @param chartSettingsPaths path(s) where customization functions are saved relative to your working directory. All charts can have initialization (e.g. myChart_Init.R) and static charts can have charting functions (e.g. myGraphic_Chart.R).   All R files in this folder are sourced and files with the correct naming convention are linked to the chart. See the Custom Charts vignette for more details. 
#'
#' 
#' @return List of elements for used to initialize the shiny app with the following parameters
#'  \itemize{
#'  \item{"meta"}{ List of configuration metadata }
#'  \item{"charts"}{ List of charts }
#'  \item{"domainData"}{ List of domain level data sets }
#'  \item{"mapping"}{ Initial Data Mapping  }
#'  \item{"standards"}{ List of domain level data standards }
#' }
#' 
#' @export
app_startup<-function(domainData=NULL, meta=NULL, charts=NULL, mapping=NULL, autoMapping=NULL, filterDomain=NULL, chartSettingsPaths=NULL){
    # If charts are not provided, load them from chartSettingsPath or the safetyCharts package
    if(is.null(charts)){
        if(is.null(chartSettingsPaths)){
            charts <- makeChartConfig()
        }else{
            charts <- makeChartConfig(chartSettingsPaths)
        }
    }

    # Prepare charts - fill in defaults, build metadata, bind functions 
    charts <- charts %>% map(prepareChart)

    # Drop charts where order is negative
    orderDrops <- charts[purrr::map_lgl(charts, function(chart) chart$order < 0)]
    if(length(orderDrops)>0){
        message("- Dropped ", length(orderDrops), " chart(s) with negative `order` parameter: ",paste(names(orderDrops),collapse=", "))
    }
    charts <- charts %>% purrr::keep(~.x$order>=0)

    # Drop charts where env is not set to safetyGraphics
    envDrops <- charts[purrr::map_lgl(charts, function(chart) !chart$envValid)]
    if(length(envDrops)>0){
        message("- Dropped ", length(envDrops), " chart(s) with `env` paramter missing or not set to 'safetyGraphics': ",paste(names(envDrops), collapse=", "))
    }
    charts <- charts %>% purrr::keep(~.x$envValid)
    
    #Drop charts if data for required domain(s) is not found
    domainDrops <- charts %>% purrr::keep(~(!all(.x$domain %in% names(domainData))))
    if(length(domainDrops)>0){
        message("- Dropped ", length(domainDrops), " chart(s) with missing data domains: ", paste(names(domainDrops), collapse=", "))
    }
    charts <- charts %>% purrr::keep(~all(.x$domain %in% names(domainData)))
    
    # sort charts based on order  
    chartOrder <- order(charts %>% map_dbl(~.x$order) %>% unlist())
    charts <- charts[chartOrder]
    
    message("- Initializing app with ",length(charts), " chart(s).")

    # Set filterDomain to NULL if specified domain doesn't exist
    if(!is.null(filterDomain)){
        if(!filterDomain %in% names(domainData)){
            message("No data found for specified filter domain of '",filterDomain,"', so filter functionality has been deactivated.")
            filterDomain<-NULL
        }
    }

    # generate a full list of metadata if none is provided
    if(is.null(meta)) meta <- makeMeta(charts)

    # generate mappings and data standards
    mappingObj <- makeMapping(domainData, meta, autoMapping, mapping)

    config<-list(
        meta=meta,
        charts=charts,
        domainData=domainData,
        mapping=mappingObj$mapping,
        standards=mappingObj$standard,
        filterDomain=filterDomain
    ) 

    return(config)
}