| OpenMS 2.5.0

Static Public Member Functions | Static Protected Member Functions | List of all members
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 (const String &tmp_path, const String &qc_output_directory, const 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
| ) |  |

inline static protected

## ◆ createCSVReport()

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

inline static

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

## ◆ 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
| ) |  |

inline static

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, SIPPeptide::mz_theo, SIPPeptide::non_zero_decomposition_coefficients, String::NONE, String::number(), OPENMS_LOG_INFO, SIPPeptide::score, SIPPeptide::sequence, AASequence::toString(), String::toUpper(), String::trim(), and SIPPeptide::unique.

## ◆ createQualityReport()

static void createQualityReport | ( | const String & | tmp_path,
|  | const String & | qc_output_directory,
|  | const 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")`
| ) |  |

inline static

References OPENMS_LOG_INFO.

## ◆ 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")`
| ) |  |

inline static

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")`
| ) |  |

inline static

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")`
| ) |  |

inline static

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
| ) |  |

inline static

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