Stereopy integration - #48
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milka1g
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josicb16 and
vladimirkovacevic
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josicb16
July 4, 2023 14:37
vladimirkovacevic
requested changes
Jul 4, 2023
| """ | ||
| stats = self.tissue.uns['cell mixtures stats'] | ||
| sc.settings.set_figure_params(dpi=300, facecolor='white') | ||
| set_figure_params(dpi=300, facecolor='white') |
Collaborator
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should it be used everywhere? Since now we have different dpis at different places in code.
| """Plot a table showing cell type abundance per cluster.""" | ||
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| sc.settings.set_figure_params(dpi=300, facecolor='white') | ||
| set_figure_params(dpi=300, facecolor='white') |
| total = total.loc[sorted(total.index.values, key=lambda x: float(x) if x != "total_cells" else float('inf'))] | ||
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| sc.settings.set_figure_params(dpi=300, facecolor='white') | ||
| set_figure_params(dpi=300, facecolor='white') |
| df = pd.concat(cells_in_comm_per_slice.values(), axis=1).fillna(0).mul(100).T | ||
| df = df[sorted(df.columns.values, key=lambda x: float(x) if x != "unknown" else float('inf'))] | ||
| sc.settings.set_figure_params(dpi=200, facecolor='white') | ||
| set_figure_params(dpi=200, facecolor='white') |
| fig, ax = plt.subplots(figsize=(20,10)) | ||
| fig.subplots_adjust(wspace=0) | ||
| sc.settings.set_figure_params(dpi=300, facecolor='white') | ||
| set_figure_params(dpi=300, facecolor='white') |
| axes = axes.ravel() | ||
| fig.subplots_adjust(wspace=0) | ||
| sc.settings.set_figure_params(dpi=300, facecolor='white') | ||
| set_figure_params(dpi=300, facecolor='white') |
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| logging.info(f'main.py took {total_time:.4f}s') | ||
| logging.warning('END') | ||
| logger.info(f'main.py took {total_time:.4f}s') |
Owner
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Cell Community Detection took... instead main.py
Owner
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Add this as warning instead info
| logging.info(f'main.py took {total_time:.4f}s') | ||
| logging.warning('END') | ||
| logger.info(f'main.py took {total_time:.4f}s') | ||
| logger.warning('END') |
| scipy==1.7.3 | ||
| seaborn~=0.11.1 | ||
| anndata==0.8.0 | ||
| tqdm>=4.60.0 |
vladimirkovacevic
approved these changes
Aug 10, 2023
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Removed scanpy as a dependency and used stereopy's function for calculating neighbor graph and leiden clustering. Updated functions to use AnnBasedStereoExpData and updated tutorial notebook. Using stereopy's logger and AlgorithmBase base class.