R/report.R

In jasenfinch/metaboReports: Automated Report Generation For Metabolomics Analyses

hash <- function(type){
  if (type == 'head') {
    headHash <- '##'
  }
  
  if (type == 'sub') {
    headHash <- '###'
  }
  return(headHash)
}

doReport <- function(analysis,parameters){
  directoryPrep(analysis,parameters)
  
  report <- c(reportHeader(analysis,parameters),
              loadData(analysis),
              overViewSection(analysis))
  
  methods <- reportMethods(class(analysis)) %>%
    {.(analysis)}
  
  if (class(analysis) == 'Workflow') {
    methods <- methods %>%
      {.(analysis)} %>%
      unlist(recursive = T)
    if (analysis %>%
        resultsProcessing() %>%
        class() == 'Binalysis') {
      binalysis <- analysis %>%
        resultsProcessing()
    }
    if (analysis %>%
        resultsProcessing() %>%
        class() == 'MetaboProfile') {
      processed <- analysis %>%
        resultsProcessing()
    }
    analysis <- analysis %>%
      resultsAnalysis()
  }
  
  
  methodSection <- map(methods,~{
    if (is.function(.)) {
      .(analysis)
    } else {
      .
    }
  })
  
  report <- c(report,
              methodSection,
              reportFooter(sessionInfo = parameters@sessionInfo)
  ) %>%
    str_c(collapse = '')
  
  title <- parameters@title %>%
    str_replace_all(' ','_')
  
  reportFile <- str_c(parameters@path,title,title,sep = '/')
  
  write_file(report,str_c(reportFile,'.Rmd'))
  
  render(str_c(reportFile,'.Rmd'))
}

#' report
#' @rdname report
#' @description Automated, dynamic report generation for a metabolomic analysis. 
#' @param analysis S4 object of class Binalysis, MetaboProfile, Analysis, Assignment or Workflow from which to genrate a report
#' @param parameters object of class ReportParameters
#' @importFrom magrittr %>%
#' @importFrom readr write_file
#' @importFrom rmarkdown render
#' @examples 
#' \dontrun{
#' library(metaboWorkflows)
#' 
#' fp <- metaboData::filePaths('FIE-HRMS','BdistachyonEcotypes') 
#' si <- metaboData::runinfo('FIE-HRMS','BdistachyonEcotypes')
#' 
#' wp <- workflowParameters('FIE-HRMS fingerprinting',fp,si,breaks = FALSE)
#'
#' analysis <- workflow(wp)
#'
#' ## For a Binalysis object
#' bd <- analysis %>%
#'  resultsProcessing()
#' p <- reportParameters('ExampleData','Steve French')
#' report(bd,p)
#' 
#' ## For an Analysis object
#' ad <- analysis %>%
#'  resultsAnalysis()
#' p <- reportParameters('ExampleData','Steve French')
#' report(ad,p) 
#' 
#' ## For an Assignment object
#' as <- analysis %>%
#'  resultsAnnotation()
#' p <- reportParameters('ExampleData','Steve French')
#' report(as,p) 
#' 
#' ## For a Workflow object
#' p <- reportParameters('ExampleData','Steve French')
#' report(analysis,p) 
#' 
#' }
#' @export

setMethod('report',signature = 'Binalysis',function(analysis,parameters){
  doReport(analysis,parameters)
})

#' @rdname report
#' @export

setMethod('report',signature = 'MetaboProfile',function(analysis,parameters){
  doReport(analysis,parameters)
})

#' @rdname report
#' @export

setMethod('report',signature = 'Analysis',function(analysis,parameters){
  doReport(analysis,parameters)
})

#' @rdname report
#' @export

setMethod('report',signature = 'Assignment',function(analysis,parameters){
  doReport(analysis,parameters)
})

#' @rdname report
#' @export

setMethod('report',signature = 'Workflow',function(analysis,parameters){
  doReport(analysis,parameters)
})