Feature/rawdata

[singjc]

This is a fairly large PR.

This implements raw targeted feature extraction from DIA/diaPASEF mzML files using a spectral library (tsv/pqp) and optionally supplemented with search results (diann tsv/osw). The extracted results can then be visualized in 1D, 2D and 3D.

Note: I do not include any test files in this branch, I will include tests later in a separate branch.

Inputs:

• Spectral library - can be either TSV or PQP
• Mass Spec Files - can be either DIA or diaPASEF data strictly in mzML format
• Search results (Optional) - can be either a DIA-NN report file or a OSW sqlite file

Plotting:

• 1D plotting - spectrum, chromatogram and mobilogram (diaPASEF) plots
• 2D plotting - heatmaps of any combination of two dimensions. Option to aggregate all precursors and fragments into a single heatmap, default is to split them into individual heatmaps.
• 3D plotting - vertical line spectrum-chromatogram plots for DIA and diaPASEF data. Aggregated 3D scatter heatmap plots of precursors and fragments, and contour plots for any two dimensions for diaPASEF data.

Loaders:

• reportLoader - TSV based search results loader (based off DIA-NNs report). TODO: need to generalize to other TSV based reports like OSW or Spectronaught
• DiaNNLoader - Loads a DIA-NN report file
• OSWLoader - Loaders OSW sqlite-based report file
• mzMLLoader - Loads an mzML file into an onDiscExperiment
• TargetedDIADataAccess - Main class that does the actual targeted extraction
• TargetDIALoader - Combines everything together to load the mzML data and perform the extraction and exports the data to a DF or TransitionGroup per precursor and per file.

Preprocess:

• transformations - moved min-max scaling to this file from the chromatogram_data_handling.py file

Server:

• RawTargetedExtractionAnalysisServer - Main script to perform targeted extraction analysis
• OneDimensionPlotterServer (Two and Three) - scripts to prepare and generate the interactive plots calling the individual interactive plotter methods from plotting

UI:

• RawTargetedExtractionAnalysisFormUI - front end user input forum for input files
• FileInputRawDataUISettings - file input settings for displaying files in the sidebar and extracting list of files if a path if given for raw data.
• RawTargetedExtractionAnalysisUI - front end for displaying components in the siderbar, i.e. search results information, extraction parameters, and for displaying plots and dataframes.

Examples

DIA (two runs)

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diaPASEF (one run)

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