Enhance GenomicFigure aesthetics and add scaling options for coverage tracks#15
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alsmith151 wants to merge 5 commits intomainfrom
Open
Enhance GenomicFigure aesthetics and add scaling options for coverage tracks#15alsmith151 wants to merge 5 commits intomainfrom
alsmith151 wants to merge 5 commits intomainfrom
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…d update GenomicFigure parameters
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This pull request introduces new normalization and scaling options for QuantNado coverage tracks, improves the flexibility of plotting, and adds convenience methods and minor bug fixes. The most important changes are grouped below by theme.
QuantNado Coverage Track Enhancements:
scaling_factor,normalise,normalize, andlibrary_sizes) toQuantNadoCoverageTrackandQuantNadoStrandedCoverageTrackfor more flexible normalization and scaling of coverage data. These parameters are now passed directly to QuantNado's extraction methods and applied to the resulting data. [1] [2] [3] [4] [5] [6] [7] [8] [9]scaling_factorand normalization options, ensuring consistent processing whether using precomputed or freshly extracted data. [1] [2]API and Usability Improvements:
defaultsmethod toGenomicFigurefor quickly applying a standard scaffold (autocolor, scalebar, and gene annotation) with optional genome and palette parameters. [1] [2]plotmethod ofGenomicFigureby sharing the x-axis among tracks, which enhances usability and consistency in the output figures.Documentation and Testing:
GenomicFigureto use Python prompt-style formatting for clarity.test_quantnado.pydemonstrating the use of the new normalization and scaling options with real data.Bug Fixes:
Dependency Update:
pandasaspdinplotnado/tracks/quantnado.pyto support new parameter types.