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updated docs
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‎docs/build/doctrees/environment.pickle‎

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‎docs/build/html/genindex.html‎

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@@ -274,10 +274,6 @@ <h2>_</h2>
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<li><a href="api/main_classes.html#SpaceTravLR.oracles.SpaceTravLR.__init__">(SpaceTravLR.oracles.SpaceTravLR method)</a>
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</li>
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<li><a href="api/main_classes.html#SpaceTravLR.spaceship.SpaceShip.__init__">(SpaceTravLR.spaceship.SpaceShip method)</a>
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</li>
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<li><a href="api/main_classes.html#SpaceTravLR.virtual_tissue.SubsampledTissue.__init__">(SpaceTravLR.virtual_tissue.SubsampledTissue method)</a>
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</li>
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<li><a href="api/main_classes.html#SpaceTravLR.virtual_tissue.VirtualTissue.__init__">(SpaceTravLR.virtual_tissue.VirtualTissue method)</a>
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</li>
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<li><a href="api/main_classes.html#SpaceTravLR.visionary.CyberBoss.__init__">(SpaceTravLR.visionary.CyberBoss method)</a>
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</li>
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<h2>C</h2>
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<table style="width: 100%" class="indextable genindextable"><tr>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="api/main_classes.html#SpaceTravLR.virtual_tissue.VirtualTissue.calculate_cell_type_alignment">calculate_cell_type_alignment() (SpaceTravLR.virtual_tissue.VirtualTissue method)</a>
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</li>
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<li><a href="api/estimator.html#SpaceTravLR.models.parallel_estimators.SpatialCellularProgramsEstimator.check_LR_properties">check_LR_properties() (SpaceTravLR.models.parallel_estimators.SpatialCellularProgramsEstimator static method)</a>
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</li>
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<li><a href="api/utilities.html#SpaceTravLR.tools.utils.clean_up_adata">clean_up_adata() (in module SpaceTravLR.tools.utils)</a>
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</ul></li>
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</ul></td>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="api/main_classes.html#SpaceTravLR.virtual_tissue.VirtualTissue.compute_branched_pseudotime">compute_branched_pseudotime() (SpaceTravLR.virtual_tissue.VirtualTissue method)</a>
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</li>
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<li><a href="api/main_classes.html#SpaceTravLR.virtual_tissue.SubsampledTissue.compute_ko_impact">compute_ko_impact() (SpaceTravLR.virtual_tissue.SubsampledTissue method)</a>
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<ul>
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<li><a href="api/main_classes.html#SpaceTravLR.virtual_tissue.VirtualTissue.compute_ko_impact">(SpaceTravLR.virtual_tissue.VirtualTissue method)</a>
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</li>
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</ul></li>
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<li><a href="api/main_classes.html#SpaceTravLR.virtual_tissue.VirtualTissue.compute_ko_impact_estimate">compute_ko_impact_estimate() (SpaceTravLR.virtual_tissue.VirtualTissue method)</a>
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</li>
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<li><a href="api/main_classes.html#SpaceTravLR.virtual_tissue.VirtualTissue.compute_vector_alignment">compute_vector_alignment() (SpaceTravLR.virtual_tissue.VirtualTissue method)</a>
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</li>
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<li><a href="api/utilities.html#SpaceTravLR.tools.utils.connectivity_to_weights">connectivity_to_weights() (in module SpaceTravLR.tools.utils)</a>
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</li>
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<li><a href="api/utilities.html#SpaceTravLR.tools.utils.convolve_by_sparse_weights">convolve_by_sparse_weights() (in module SpaceTravLR.tools.utils)</a>
@@ -437,8 +419,6 @@ <h2>G</h2>
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<li><a href="api/main_classes.html#SpaceTravLR.gene_factory.GeneFactory.get_ko_data">get_ko_data() (SpaceTravLR.gene_factory.GeneFactory static method)</a>
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</li>
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<li><a href="api/main_classes.html#SpaceTravLR.spaceship.SpaceShip.get_nichenet_links_">get_nichenet_links_() (SpaceTravLR.spaceship.SpaceShip method)</a>
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</li>
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<li><a href="api/main_classes.html#SpaceTravLR.virtual_tissue.VirtualTissue.get_umap_centroid_cells">get_umap_centroid_cells() (SpaceTravLR.virtual_tissue.VirtualTissue method)</a>
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</li>
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</ul></td>
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</tr></table>
@@ -449,17 +429,13 @@ <h2>I</h2>
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<table style="width: 100%" class="indextable genindextable"><tr>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="api/main_classes.html#SpaceTravLR.oracles.SpaceTravLR.imbue_adata_with_space">imbue_adata_with_space() (SpaceTravLR.oracles.SpaceTravLR static method)</a>
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</li>
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<li><a href="api/main_classes.html#SpaceTravLR.virtual_tissue.VirtualTissue.init_cartography">init_cartography() (SpaceTravLR.virtual_tissue.VirtualTissue method)</a>
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</li>
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<li><a href="api/estimator.html#SpaceTravLR.models.parallel_estimators.SpatialCellularProgramsEstimator.init_data">init_data() (SpaceTravLR.models.parallel_estimators.SpatialCellularProgramsEstimator method)</a>
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</li>
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<li><a href="api/main_classes.html#SpaceTravLR.virtual_tissue.VirtualTissue.init_gene_factory">init_gene_factory() (SpaceTravLR.virtual_tissue.VirtualTissue method)</a>
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<li><a href="api/utilities.html#SpaceTravLR.models.parallel_estimators.init_received_ligands">init_received_ligands() (in module SpaceTravLR.models.parallel_estimators)</a>
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</li>
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</ul></td>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="api/utilities.html#SpaceTravLR.models.parallel_estimators.init_received_ligands">init_received_ligands() (in module SpaceTravLR.models.parallel_estimators)</a>
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<li><a href="api/main_classes.html#SpaceTravLR.spaceship.SpaceShip.interactive_select">interactive_select() (SpaceTravLR.spaceship.SpaceShip method)</a>
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</li>
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<li><a href="api/main_classes.html#SpaceTravLR.oracles.OracleQueue.is_empty">is_empty (SpaceTravLR.oracles.OracleQueue property)</a>
@@ -499,26 +475,22 @@ <h2>L</h2>
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<li><a href="api/estimator.html#SpaceTravLR.models.parallel_estimators.SpatialCellularProgramsEstimator.load">load() (SpaceTravLR.models.parallel_estimators.SpatialCellularProgramsEstimator method)</a>
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</li>
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<li><a href="api/main_classes.html#SpaceTravLR.spaceship.SpaceShip.load_base_cell_thresholds">load_base_cell_thresholds() (SpaceTravLR.spaceship.SpaceShip method)</a>
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</li>
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<li><a href="api/main_classes.html#SpaceTravLR.spaceship.SpaceShip.load_base_GRN">load_base_GRN() (SpaceTravLR.spaceship.SpaceShip static method)</a>
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</li>
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</ul></td>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="api/main_classes.html#SpaceTravLR.spaceship.SpaceShip.load_base_GRN">load_base_GRN() (SpaceTravLR.spaceship.SpaceShip static method)</a>
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</li>
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<li><a href="api/main_classes.html#SpaceTravLR.beta.Betabase.load_betadata">load_betadata() (SpaceTravLR.beta.Betabase method)</a>
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<ul>
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<li><a href="api/main_classes.html#SpaceTravLR.gene_factory.GeneFactory.load_betadata">(SpaceTravLR.gene_factory.GeneFactory static method)</a>
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</li>
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<li><a href="api/main_classes.html#SpaceTravLR.virtual_tissue.VirtualTissue.load_betadata">(SpaceTravLR.virtual_tissue.VirtualTissue method)</a>
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</li>
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<li><a href="api/main_classes.html#SpaceTravLR.visionary.Visionary.load_betadata">(SpaceTravLR.visionary.Visionary static method)</a>
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</li>
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</ul></li>
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<li><a href="api/main_classes.html#SpaceTravLR.gene_factory.GeneFactory.load_betas">load_betas() (SpaceTravLR.gene_factory.GeneFactory method)</a>
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</li>
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<li><a href="api/main_classes.html#SpaceTravLR.beta.Betabase.load_betas_from_disk">load_betas_from_disk() (SpaceTravLR.beta.Betabase method)</a>
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<li><a href="api/main_classes.html#SpaceTravLR.virtual_tissue.VirtualTissue.load_knockout_gex">load_knockout_gex() (SpaceTravLR.virtual_tissue.VirtualTissue method)</a>
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</li>
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</ul></td>
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</tr></table>
@@ -555,22 +527,10 @@ <h2>P</h2>
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</li>
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</ul></li>
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<li><a href="api/main_classes.html#SpaceTravLR.gene_factory.GeneFactory.perturb_batch">perturb_batch() (SpaceTravLR.gene_factory.GeneFactory method)</a>
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<li><a href="api/main_classes.html#SpaceTravLR.virtual_tissue.VirtualTissue.plot_arrows">plot_arrows() (SpaceTravLR.virtual_tissue.VirtualTissue method)</a>
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<li><a href="api/main_classes.html#SpaceTravLR.virtual_tissue.VirtualTissue.plot_arrows_pseudotime">plot_arrows_pseudotime() (SpaceTravLR.virtual_tissue.VirtualTissue method)</a>
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</li>
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<li><a href="api/main_classes.html#SpaceTravLR.virtual_tissue.VirtualTissue.plot_comparative_bar">plot_comparative_bar() (SpaceTravLR.virtual_tissue.VirtualTissue method)</a>
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</li>
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</ul></td>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="api/main_classes.html#SpaceTravLR.virtual_tissue.VirtualTissue.plot_comparative_radar">plot_comparative_radar() (SpaceTravLR.virtual_tissue.VirtualTissue method)</a>
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</li>
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<li><a href="api/main_classes.html#SpaceTravLR.virtual_tissue.VirtualTissue.plot_gene_vs_proximity">plot_gene_vs_proximity() (SpaceTravLR.virtual_tissue.VirtualTissue method)</a>
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</li>
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<li><a href="api/estimator.html#SpaceTravLR.models.parallel_estimators.SpatialCellularProgramsEstimator.plot_modulators">plot_modulators() (SpaceTravLR.models.parallel_estimators.SpatialCellularProgramsEstimator method)</a>
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</li>
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<li><a href="api/main_classes.html#SpaceTravLR.virtual_tissue.VirtualTissue.plot_radar">plot_radar() (SpaceTravLR.virtual_tissue.VirtualTissue method)</a>
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</li>
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<li><a href="api/main_classes.html#SpaceTravLR.gene_factory.GeneFactory.possible_targets">possible_targets (SpaceTravLR.gene_factory.GeneFactory property)</a>
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</li>
@@ -584,8 +544,6 @@ <h2>P</h2>
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<h2>R</h2>
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<table style="width: 100%" class="indextable genindextable"><tr>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="api/main_classes.html#SpaceTravLR.virtual_tissue.VirtualTissue.random_color">random_color() (SpaceTravLR.virtual_tissue.VirtualTissue method)</a>
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</li>
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<li><a href="api/utilities.html#SpaceTravLR.models.parallel_estimators.received_ligands">received_ligands() (in module SpaceTravLR.models.parallel_estimators)</a>
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</li>
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<li><a href="api/main_classes.html#SpaceTravLR.visionary.CyberBoss.reformat">reformat() (SpaceTravLR.visionary.CyberBoss method)</a>
@@ -596,10 +554,10 @@ <h2>R</h2>
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</ul></li>
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<li><a href="api/main_classes.html#SpaceTravLR.oracles.OracleQueue.regulated_genes">regulated_genes (SpaceTravLR.oracles.OracleQueue property)</a>
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</li>
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</ul></td>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="api/main_classes.html#SpaceTravLR.oracles.OracleQueue.remaining_genes">remaining_genes (SpaceTravLR.oracles.OracleQueue property)</a>
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</li>
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</ul></td>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="api/main_classes.html#SpaceTravLR.astronomer.Astronaut.run">run() (SpaceTravLR.astronomer.Astronaut method)</a>
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<ul>
@@ -623,17 +581,13 @@ <h2>S</h2>
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<li><a href="api/main_classes.html#SpaceTravLR.spaceship.SpaceShip.setup_">setup_() (SpaceTravLR.spaceship.SpaceShip method)</a>
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</li>
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<li><a href="api/main_classes.html#SpaceTravLR.spaceship.SpaceShip.setup_perturbations">setup_perturbations() (SpaceTravLR.spaceship.SpaceShip method)</a>
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</li>
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<li><a href="api/main_classes.html#SpaceTravLR.virtual_tissue.VirtualTissue.signature2gradient">signature2gradient() (SpaceTravLR.virtual_tissue.VirtualTissue method)</a>
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</li>
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<li><a href="api/main_classes.html#SpaceTravLR.virtual_tissue.VirtualTissue.smooth_over_manifold">smooth_over_manifold() (SpaceTravLR.virtual_tissue.VirtualTissue method)</a>
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</li>
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<li><a href="api/main_classes.html#SpaceTravLR.spaceship.SpaceShip">SpaceShip (class in SpaceTravLR.spaceship)</a>
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</li>
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</ul></td>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="api/main_classes.html#SpaceTravLR.oracles.SpaceTravLR">SpaceTravLR (class in SpaceTravLR.oracles)</a>
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</li>
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</ul></td>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="api/estimator.html#SpaceTravLR.models.parallel_estimators.SpatialCellularProgramsEstimator">SpatialCellularProgramsEstimator (class in SpaceTravLR.models.parallel_estimators)</a>
638592
</li>
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<li><a href="api/main_classes.html#SpaceTravLR.spaceship.SpaceShip.spawn_worker">spawn_worker() (SpaceTravLR.spaceship.SpaceShip method)</a>
@@ -644,8 +598,6 @@ <h2>S</h2>
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<li><a href="api/main_classes.html#SpaceTravLR.visionary.Visionary.splash_betas">(SpaceTravLR.visionary.Visionary method)</a>
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</li>
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</ul></li>
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<li><a href="api/main_classes.html#SpaceTravLR.virtual_tissue.SubsampledTissue">SubsampledTissue (class in SpaceTravLR.virtual_tissue)</a>
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</li>
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</ul></td>
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</tr></table>
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</section>
@@ -663,10 +615,6 @@ <h2>U</h2>
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<section id="V" class="genindex-section">
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<h2>V</h2>
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<table style="width: 100%" class="indextable genindextable"><tr>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="api/main_classes.html#SpaceTravLR.virtual_tissue.VirtualTissue">VirtualTissue (class in SpaceTravLR.virtual_tissue)</a>
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</li>
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</ul></td>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="api/main_classes.html#SpaceTravLR.visionary.Visionary">Visionary (class in SpaceTravLR.visionary)</a>
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</li>

‎docs/build/html/index.html‎

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@@ -440,6 +440,6 @@ <h2>Analysis<a class="headerlink" href="#analysis" title="Link to this heading">
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<script src="_static/design-tabs.js?v=f930bc37"></script>
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<script defer="defer" src="https://unpkg.com/@popperjs/core@2"></script>
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<script defer="defer" src="https://unpkg.com/tippy.js@6"></script>
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<script defer="defer" src="_static/tippy/index.699453fa-e914-4031-ab10-2261daf3f152.js"></script>
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<script defer="defer" src="_static/tippy/index.64a69862-deed-45f9-a9da-f2f5e9eb28ac.js"></script>
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</body>
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</html>

‎docs/build/html/objects.inv‎

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‎docs/build/html/searchindex.js‎

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‎docs/source/ligand_perturbation.ipynb‎

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‎docs/source/ligand_receptor_interactions.ipynb‎

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"metadata": {},
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"outputs": [],
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"source": [
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"%load_ext autoreload\n",
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"%autoreload 2\n",
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"%config InlineBackend.figure_format = 'retina'"
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]
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},
@@ -65,35 +67,18 @@
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"execution_count": null,
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"id": "0cf3181a",
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"AnnData object with n_obs × n_vars = 4804 × 3396\n",
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" obs: 'X', 'Y', 'cell_type', 'author_cell_type', 'cell_type_int'\n",
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" uns: 'author_cell_type_colors', 'cell_thresholds', 'neighbors', 'pca', 'received_ligands', 'received_ligands_tfl', 'umap'\n",
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" obsm: 'X_pca', 'X_umap', 'spatial', 'spatial_unscaled'\n",
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" varm: 'PCs'\n",
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" layers: 'imputed_count', 'normalized_count'\n",
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" obsp: 'connectivities', 'distances'"
82-
]
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},
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"execution_count": 4,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"outputs": [],
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"source": [
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"adata = sc.read_h5ad('/Volumes/SSD/training_data/snrna_human_melanoma.h5ad')\n",
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"adata"
9277
]
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},
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{
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"cell_type": "code",
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"execution_count": 5,
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"execution_count": null,
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"id": "c5bc12f5",
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"metadata": {},
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"outputs": [],

‎src/SpaceTravLR/virtual_tissue.py‎

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Original file line numberDiff line numberDiff line change
@@ -23,6 +23,41 @@
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from .gene_factory import GeneFactory
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from .beta import BetaFrame
2525

26+
class suppress_stdout_stderr(object):
27+
def __enter__(self):
28+
self.outnull_file = open(os.devnull, 'w')
29+
self.errnull_file = open(os.devnull, 'w')
30+
31+
self.old_stdout_fileno_undup = sys.stdout.fileno()
32+
self.old_stderr_fileno_undup = sys.stderr.fileno()
33+
34+
self.old_stdout_fileno = os.dup ( sys.stdout.fileno() )
35+
self.old_stderr_fileno = os.dup ( sys.stderr.fileno() )
36+
37+
self.old_stdout = sys.stdout
38+
self.old_stderr = sys.stderr
39+
40+
os.dup2 ( self.outnull_file.fileno(), self.old_stdout_fileno_undup )
41+
os.dup2 ( self.errnull_file.fileno(), self.old_stderr_fileno_undup )
42+
43+
sys.stdout = self.outnull_file
44+
sys.stderr = self.errnull_file
45+
return self
46+
47+
def __exit__(self, *_):
48+
sys.stdout = self.old_stdout
49+
sys.stderr = self.old_stderr
50+
51+
os.dup2 ( self.old_stdout_fileno, self.old_stdout_fileno_undup )
52+
os.dup2 ( self.old_stderr_fileno, self.old_stderr_fileno_undup )
53+
54+
os.close ( self.old_stdout_fileno )
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os.close ( self.old_stderr_fileno )
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self.outnull_file.close()
58+
self.errnull_file.close()
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2661
def normalize_gradient(gradient, method="sqrt"):
2762
if method == "sqrt":
2863
size = np.sqrt(np.power(gradient, 2).sum(axis=1))
@@ -815,6 +850,9 @@ def smooth_over_manifold(self, obs_key, k=15, use_rep='X_umap', new_key_suffix='
815850
def compute_branched_pseudotime(self, pairs, annot, source_cell_type, knn=10, n_components=5, n_source_cells=20):
816851
import scanpy.external as sce
817852

853+
if 'X_pca' not in self.adata.obsm:
854+
sc.pp.pca(self.adata)
855+
818856
if 'pseudotime' in self.adata.obs:
819857
del self.adata.obs['pseudotime']
820858

@@ -827,7 +865,9 @@ def compute_branched_pseudotime(self, pairs, annot, source_cell_type, knn=10, n_
827865
for pair in pairs:
828866
_adata = adata[adata.obs[annot].isin([pair[0], pair[1]])].copy()
829867

830-
sce.tl.palantir(_adata, n_components=n_components, knn=knn)
868+
with suppress_stdout_stderr():
869+
print('!!!!')
870+
sce.tl.palantir(_adata, n_components=n_components, knn=knn)
831871

832872
for ij, cell in enumerate(source_cells):
833873
pltr = sce.tl.palantir_results(

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