R/writeExtras.R

In biodavidjm/artMS: Analytical R tools for Mass Spectrometry

# ------------------------------------------------------------------------------
# @title Write extras
# @description Extras after MSstats, as annotations, volcano plots, heatmaps
# @param results MSstats results
# @param config The configuration object (yaml)
# 
# @return Extras as selected in the yaml file, including:
# - volcano plot (pdf)
# - Adding annotations (gene symbol based on uniprot)
# @keywords extras, annotations, volcano
.artms_writeExtras <- function(results, 
                               config,
                               verbose = TRUE) {
  
  if (length(results) == 0 | !exists('results')) {
    stop("No results found to annotate!")
  }
  
  # Annotation
  if (config$output_extras$annotate$enabled) {
    message(">> ANNOTATING THE RESULTS (adding gene symbols and protein names)")
    if(!is.null(config$output_extras$annotate$species)){
      results_ann <- artmsAnnotationUniprot(x = results, 
                                            columnid = 'Protein', 
                                            species = config$output_extras$annotate$species)
      output_annotated_file <- gsub(".txt", "-annotated.txt", config$files$output)
      write.table(results_ann, output_annotated_file, quote = FALSE, 
                  row.names = FALSE, 
                  col.names = TRUE, 
                  sep = "\t")
    } else {
      if(verbose) message("--- Cannot find species name in the file name 
(Add specie to field 'output_extras > annotate > species' in the config file)")
      results_ann <- results
    }
  }else{
    results_ann <- results
  }
  
  lfc_lower <- as.numeric(unlist(strsplit(config$output_extras$plots$LFC, split = " "))[1])
  lfc_upper <- as.numeric(unlist(strsplit(config$output_extras$plots$LFC, split = " "))[2])
  
  ## This option was originally available in the config file but
  ## it was removed
  config$output_extras$plots$comparisons <- "all"
  ## ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  
  selected_labels <- config$output_extras$plots$comparisons
  if (is.null(selected_labels) || selected_labels == 'all') 
    selected_labels = '*'
  
  # remove the Inf, -Inf log2FC hits.
  results_ann <- results_ann[!is.infinite(results_ann$log2FC), ]
  
  ## select data points  by LFC & FDR criterium in single condition and
  ## adding corresponding data points from the other conditions
  sign_hits <- .artms_significantHits(results_ann,
                                      labels = selected_labels,
                                      LFC = c(lfc_lower, lfc_upper),
                                      FDR = config$output_extras$plots$FDR)

  if (dim(sign_hits)[1] == 0){
    message("--(-) No significant hits detected in this experiment. aborting plots. ")
  }else{
    sign_labels <- unique(sign_hits$Label)
    if(verbose) message( sprintf(
      "-- Selected hits for plots with LFC between %s and %s at %s FDR:%s ",
      lfc_lower,
      lfc_upper,
      config$output_extras$plots$FDR,
      nrow(sign_hits) / length(sign_labels)))
    
    ## REPRESENTING RESULTS AS HEATMAP, if enabled
    if (config$output_extras$plots$heatmap) {
      # Heatmap only for > 1 comparison
      if (dim(sign_hits)[1] > 1) {
        if(verbose) message(">> PLOTTING HEATMAP FOR SIGNIFICANT CHANGES ")
        heat_labels <- .artms_prettyPrintHeatmapLabels(uniprot_acs = sign_hits$Protein,
                                                       uniprot_ids = sign_hits$name,
                                                       gene_names = sign_hits$Gene.names)
          
        heat_data_w <- .artms_plotHeat(mss_F = sign_hits,
                                       out_file =  gsub('.txt', '-sign.pdf', config$files$output),
                                       names = heat_labels,
                                       cluster_cols = config$output_extras$plots$heatmap_cluster_cols,
                                       display = config$output_extras$plots$heatmap_display,
                                       verbose = verbose)
      }
    }
  }
  
  if (config$output_extras$plots$volcano) {
    if(verbose) message(">> PLOTTING VOLCANO PLOT ")
    file_name <- gsub('.txt', '-volcano.pdf', config$files$output)
    artmsVolcanoPlot(
      mss_results = results_ann[grep(selected_labels, results_ann$Label), ], 
      lfc_upper = lfc_upper, lfc_lower = lfc_lower, 
      FDR = config$output_extras$plots$FDR,
      output_name = file_name,
      verbose = verbose
    )
  }
}