Method plotScoresAndWeights

src/topp/MetaProSIP.cpp:667–765

  }

  static void plotScoresAndWeights(const String& output_dir, const String& tmp_path, const String& file_suffix, const String& file_extension, const vector<SIPPeptide>& sip_peptides, double score_plot_yaxis_min, Size debug_level = 0, const QString& executable = QString("R"))
  {
    String score_filename = String("score_plot") + file_suffix + file_extension;
    String script_filename = String("score_plot") + file_suffix + String(".R");

    for (Size i = 0; i != sip_peptides.size(); ++i)
    {
      TextFile current_script;
      StringList rate_dec_list;
      StringList rate_corr_list;
      StringList weights_list;
      StringList corr_list;

      for (MapRateToScoreType::const_iterator mit = sip_peptides[i].decomposition_map.begin(); mit != sip_peptides[i].decomposition_map.end(); ++mit)
      {
        rate_dec_list.push_back(String(mit->first));
        weights_list.push_back(String(mit->second));
      }

      for (MapRateToScoreType::const_iterator mit = sip_peptides[i].correlation_map.begin(); mit != sip_peptides[i].correlation_map.end(); ++mit)
      {
        rate_corr_list.push_back(String(mit->first));
        corr_list.push_back(String(mit->second));
      }

      String rate_dec_list_string;
      rate_dec_list_string.concatenate(rate_dec_list.begin(), rate_dec_list.end(), ",");

      String weights_list_string;
      weights_list_string.concatenate(weights_list.begin(), weights_list.end(), ",");

      String rate_corr_list_string;
      rate_corr_list_string.concatenate(rate_corr_list.begin(), rate_corr_list.end(), ",");

      String corr_list_string;
      corr_list_string.concatenate(corr_list.begin(), corr_list.end(), ",");

      current_script.addLine("rate_dec<-c(" + rate_dec_list_string + ")");
      current_script.addLine("dec<-c(" + weights_list_string + ")");
      current_script.addLine("if (max(dec)!=0) {dec<-dec/max(dec)}");
      current_script.addLine("rate_corr<-c(" + rate_corr_list_string + ")");
      current_script.addLine("corr<-c(" + corr_list_string + ")");

      if (score_plot_yaxis_min >= 0)
      {
        current_script.addLine("corr[corr<0]=0"); // truncate at 0 for better drawing
      }

      current_script.addLine("x0=rate_dec; x1=rate_dec; y0=rep(0, length(x0)); y1=dec"); // create R segments for decomposition score (vertical bars)
      if (file_extension == "png")
      {
        current_script.addLine("png('" + tmp_path + "/" + score_filename + "')");
      }
      else if (file_extension == "svg")
      {
        current_script.addLine("svg('" + tmp_path + "/" + score_filename + "', width=8, height=4.5)");
      }
      else if (file_extension == "pdf")