MetaProSIPReporting Class Reference

Static Public Member Functions
static void	plotHeatMap (const String &output_dir, const String &tmp_path, const String &file_suffix, const String &file_extension, const vector< vector< double > > &binned_ria, vector< String > class_labels, Size debug_level=0, const QString &executable=QString("R"))
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"))
static void	writeHTML (const String &qc_output_directory, const String &file_suffix, const String &file_extension, const vector< SIPPeptide > &sip_peptides)
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"))
static void	createQualityReport (String tmp_path, String qc_output_directory, String file_suffix, const String &file_extension, const vector< vector< SIPPeptide > > &sip_peptide_cluster, Size n_heatmap_bins, double score_plot_y_axis_min, bool report_natural_peptides, const QString &executable=QString("R"))
static void	createCSVReport (vector< vector< SIPPeptide > > &sippeptide_cluster, ofstream &os, map< String, String > &proteinid_to_description)
static void	createPeptideCentricCSVReport (const String in_mzML, const String &file_extension, vector< vector< SIPPeptide > > &sippeptide_cluster, ofstream &os, map< String, String > &proteinid_to_description, String qc_output_directory, String file_suffix, bool report_natural_peptides)

Static Protected Member Functions
static void	createBinnedPeptideRIAData_ (const Size n_heatmap_bins, const vector< vector< SIPPeptide > > &sip_clusters, vector< vector< double > > &binned_peptide_ria, vector< String > &cluster_labels)

Member Function Documentation

createBinnedPeptideRIAData_()

static void createBinnedPeptideRIAData_ ( const Size  n_heatmap_bins, const vector< vector< SIPPeptide > > &  sip_clusters, vector< vector< double > > &  binned_peptide_ria, vector< String > &  cluster_labels  )

inlinestaticprotected

createCSVReport()

static void createCSVReport ( vector< vector< SIPPeptide > > &  sippeptide_cluster, ofstream &  os, map< String, String > &  proteinid_to_description  )

inlinestatic

References SIPPeptide::accessions, OpenMS::Constants::k, OpenMS::Math::median(), String::NONE, String::number(), SIPPeptide::sequence, AASequence::toUnmodifiedString(), String::toUpper(), String::trim(), and SIPPeptide::unique.

Referenced by TOPPMetaProSIP::main_().

createPeptideCentricCSVReport()

static void createPeptideCentricCSVReport ( const String  in_mzML, const String &  file_extension, vector< vector< SIPPeptide > > &  sippeptide_cluster, ofstream &  os, map< String, String > &  proteinid_to_description, String  qc_output_directory, String  file_suffix, bool  report_natural_peptides  )

inlinestatic

References SIPPeptide::accessions, SIPPeptide::accumulated, SIPPeptide::charge, SIPPeptide::explained_TIC_fraction, SIPPeptide::feature_mz, SIPPeptide::feature_rt, SIPPeptide::feature_type, SIPPeptide::global_LR, SIPPeptide::incorporations, OpenMS::Constants::k, LOG_INFO, SIPPeptide::mz_theo, SIPPeptide::non_zero_decomposition_coefficients, String::NONE, String::number(), SIPPeptide::score, SIPPeptide::sequence, AASequence::toString(), String::toUpper(), String::trim(), and SIPPeptide::unique.

Referenced by TOPPMetaProSIP::main_().

createQualityReport()

static void createQualityReport ( String  tmp_path, String  qc_output_directory, String  file_suffix, const String &  file_extension, const vector< vector< SIPPeptide > > &  sip_peptide_cluster, Size  n_heatmap_bins, double  score_plot_y_axis_min, bool  report_natural_peptides, const QString &  executable = QString("R")  )

inlinestatic

References LOG_INFO.

Referenced by TOPPMetaProSIP::main_().

plotFilteredSpectra()

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")  )

inlinestatic

References TextFile::addLine(), String::concatenate(), Peak1D::getIntensity(), Peak1D::getMZ(), TextFile::store(), and String::toQString().

plotHeatMap()

static void plotHeatMap ( const String &  output_dir, const String &  tmp_path, const String &  file_suffix, const String &  file_extension, const vector< vector< double > > &  binned_ria, vector< String >  class_labels, Size  debug_level = 0, const QString &  executable = QString("R")  )

inlinestatic

References TextFile::addLine(), String::concatenate(), TextFile::store(), and String::toQString().

plotScoresAndWeights()

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")  )

inlinestatic

References TextFile::addLine(), String::concatenate(), TextFile::store(), and String::toQString().

writeHTML()

static void writeHTML ( const String &  qc_output_directory, const String &  file_suffix, const String &  file_extension, const vector< SIPPeptide > &  sip_peptides  )

inlinestatic

References SIPIncorporation::abundance, TextFile::addLine(), SIPIncorporation::correlation, OpenMS::Constants::k, String::number(), SIPIncorporation::rate, TextFile::store(), and String::toQString().