API

Note: This section provides a comprehensive overview of all methods and classes avaliable in MassDash. This content is generated automatically using sphinx autosummary and autodoc based on the python documentation.

massdash.structs: Internal Structures For storing data

massdash/structs

Internal Data Structures for storing data

Abstract Classes

structs.Data1D	Abstract class of storing a 1D data set where have the data vs intensity
structs.GenericFeature	This is a generic peak picker class which should serve as an abstract class which future peak pickers can easily be added
structs.GenericStructCollection	Dictionary like object where keys are the run names and values are the data structures.

Classes

structs.Chromatogram	A single chromatogram object storing retention time and intensity data.
structs.Mobilogram	A single mobilogram object storing intensity and ion mobility data.
structs.Spectrum	A single spectrum object storing mz and intensity data.
structs.TransitionGroup	A Transition Group which contains a list of precursor and transition data.
structs.TransitionGroupFeature	An object storing attributes on the detected feature in a TransitionGroup.
structs.TransitionFeature	An object storing attributes on the detected feature in a Transition
structs.FeatureMap	Class for storing a feature map a feature map only contains the following columns: - mz: mass to charge ratio - rt: retention time - im: ion mobility - int: intensity - ms_level: 1 for precursor, 2 for fragment - annotation: annotation of precursor/fragment
structs.TargetedDIAConfig	A class representing the configuration for the extraction windows.

Collections

structs.TransitionGroupCollection	A collection of TransitionGroups Objects with the Mapping <RunName>:<TransitionGroup>
structs.TransitionGroupFeatureCollection	A collection of TransitionGroupFeature Objects with the Mapping <RunName>:List[<TransitionGroupFeature>]
structs.FeatureMapCollection	A collection of FeatureMap Objects with the Mapping <RunName>:<FeatureMap>
structs.TopTransitionGroupFeatureCollection	A collection of TransitionGroups Objects with the Mapping <RunName>:<TransitionGroupFeature> Note: unlike TransitionGroupFeatureCollection, the keys are not a list of TransitionGroupFeatures, just a single TransitionGroupFeature

massdash.loaders: Classes for loading data

massdash/loaders

The massdash.loaders subpackage contains the structures for loading data into MassDash

Abstract Classes

GenericChromatogramLoader	Abstract class for loading raw chromatogram data
GenericSpectrumLoader	Abstract class for loading raw spectrum data

Classes

ResultsLoader	Class for loading Results files.
MzMLDataLoader	Class to load data from MzMLFiles using a .osw output file or .tsv report file
OpenSwathXICParquetLoader	Class for loading Chromatograms and peak features from XIC (PyProphet) parquet files and a results files.
SqMassLoader	Class for loading Chromatograms and peak features from SqMass files and OSW files Inherits from GenericChromatogramLoader
XICParquetDataLoader	Class for loading Chromatograms and peak features from DIA-NNs results and XIC parquet files Inherits from GenericChromatogramLoader
SpectralLibraryLoader	Class for loading spectral library files.

massdash.loaders.access: Classes For Low Level Data Access

massdash/loaders/access

The massdash.loaders.access subpackage contains the low level access to DIA data files.

Abstract Classes

GenericResultsAccess

Abstract class for accessing results from a generic results file.

Classes

SqMassDataAccess
MzMLDataAccess	Class for data loading and extracting operations of an .mzML file
OSWDataAccess	A class for accessing data from an OpenSWATH SQLite database.
OSWPQResultsAccess	Class for accessing .oswpq directory containing precursors_features.parquet and transition_features.parquet files.
OpenSwathXICParquetAccess
ResultsTSVDataAccess	Class for generic access to TSV file containing the results, currently only supports DIA-NN tsv files
TransitionPQPDataAccess	Class to load a transition PQP file
TransitionTSVDataAccess	Class to load a transition TSV file
XICParquetDataAccess	Class for accessing XIC Parquet files (DIA-NN output)

Abstract Classes

GenericResultsAccess

Abstract class for accessing results from a generic results file.

massdash.plotting: Classes for plotting data

massdash/plotting

This subpackage contains classes for plotting

Abstract Classes

GenericPlotter

A Generic plotter abstract class.

Classes

PlotConfig	A class representing the configuration for a plot.
InteractivePlotter	Class for generating interactive plots using Bokeh.
InteractiveTwoDimensionPlotter	A class for interactive two-dimensional plotting.
InteractiveThreeDimensionPlotter	Class for interactive three-dimensional plotting.

massdash.peakPickers: Classes for Peak Picking

massdash/peakPickers

This subpackage contains classes for performing peak picking

Abstract Classes

GenericPeakPicker

This is a generic peak picker class which should serve as an abstract class which future peak pickers can easily be added

Classes

MRMTransitionGroupPicker	python wrapper of the pyopenms MRMTransitionGroupPicker
pyMRMTransitionGroupPicker	This is a python implementation based on OpenMS peak picker
ConformerPeakPicker	Class for performing peak picking using the Conformer model.

massdash.testing: Classes for testing

massdash/testing

This package contains classes for testing massdash. SnapShotExtension classes are based off of syrupy snapshots

NumpySnapshotExtension	Handles Numpy Snapshots.
PandasSnapshotExtension	Handles Pandas Snapshots.
BokehSnapshotExtension	Handles Bokeh Snapshots.
PlotlySnapshotExtension	Handles Plotly Snapshots.