Method plotFilteredSpectra

src/topp/MetaProSIP.cpp:468–544

  }

  static void plotFilteredSpectra(const String& output_dir, const String& tmp_path, const String& file_suffix, const String& file_extension, const vector<SIPPeptide>& sip_peptides, Size debug_level = 0, const QString& executable = QString("R"))
  {
    String filename = String("spectrum_plot") + file_suffix + "." + file_extension;
    String script_filename = String("spectrum_plot") + file_suffix + String(".R");

    for (Size i = 0; i != sip_peptides.size(); ++i)
    {
      TextFile current_script;
      StringList mz_list;
      StringList intensity_list;

      for (Size j = 0; j != sip_peptides[i].accumulated.size(); ++j)
      {
        const Peak1D& peak = sip_peptides[i].accumulated[j];
        mz_list.push_back(String(peak.getMZ()));
        intensity_list.push_back(String(peak.getIntensity()));
      }

      String mz_list_string;
      mz_list_string.concatenate(mz_list.begin(), mz_list.end(), ",");

      String intensity_list_string;
      intensity_list_string.concatenate(intensity_list.begin(), intensity_list.end(), ",");

      current_script.addLine("mz<-c(" + mz_list_string + ")");
      current_script.addLine("int<-c(" + intensity_list_string + ")");
      current_script.addLine("x0=mz; x1=mz; y0=rep(0, length(x0)); y1=int");

      if (file_extension == "png")
      {
        current_script.addLine("png('" + tmp_path + "/" + filename + "')");
      }
      else if (file_extension == "svg")
      {
        current_script.addLine("svg('" + tmp_path + "/" + filename + "', width=8, height=4.5)");
      }
      else if (file_extension == "pdf")
      {
        current_script.addLine("pdf('" + tmp_path + "/" + filename + "', width=8, height=4.5)");
      }

      current_script.addLine("plot.new()");
      current_script.addLine("plot.window(xlim=c(min(mz),max(mz)), ylim=c(0,max(int)))");
      current_script.addLine("axis(1); axis(2)");
      current_script.addLine("title(xlab=\"m/z\")");
      current_script.addLine("title(ylab=\"intensity\")");
      current_script.addLine("box()");
      current_script.addLine("segments(x0,y0,x1,y1)");
      current_script.addLine("tmp<-dev.off()");
      current_script.store(tmp_path + "/" + script_filename);

      QProcess p;
      QStringList env = QProcess::systemEnvironment();
      env << QString("R_LIBS=") + tmp_path.toQString();
      p.setEnvironment(env);

      QStringList qparam;
      qparam << "--vanilla" << "--quiet" << "--slave" << "--file=" + QString(tmp_path.toQString() + "/" + script_filename.toQString());