merge to master #24
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merge to master #24
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- All tracks now inherit from Track base class
- with three method:
- plot(ax, gr: GenomeRange, **kwargs) # all gr doest not support str input
- fetch_plot_data(gr: GenomeRange, **kwargs) # gr2, resolution, normalize ... can be passed in kwargs
- fetch_data(gr: GenomeRange, **kwargs)
- Different types of plotting style are implemented in BaseTrack's mixin class.
- Docs now can be build during inheritance, however this is not implemented yet
- Features now should be used like: Feature(color="xxx", name="xxx")
- galleries not tested:
- [ ] decay
- [ ] hicdiff
- [ ] reso_normalize
- [ ] selfish
- [ ] smoothing
-
restore requiremnts.txt
- Causes:
- Other changes:
- add repr method for GenomeRange
- HicMatBase now set all processing parameters and norm parameter to False
- Cool and DotHic now set transform to log and norm to False as default
- Change PlotHiC.norm to properties['norm'] for simplicity
- Add plot_gr and plot_gr2 properties in HicMatBase to store the original plot GenomeRange
- otherwise the genome_range will be expanded two times in HicDiff by calling fetch_plot_data
- Add `gr_updated` paramerter in HiCMatBase.fetch_plot_data.kwargs to avoid re-expand GenomeRanges in HiCDiff/Selfish
zhqu1148980644
approved these changes
Jan 25, 2021
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