iplotx 0.9.0__tar.gz → 0.10.0__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {iplotx-0.9.0 → iplotx-0.10.0}/.github/workflows/test.yml +1 -4
- {iplotx-0.9.0 → iplotx-0.10.0}/PKG-INFO +1 -2
- {iplotx-0.9.0 → iplotx-0.10.0}/docs/source/sg_execution_times.rst +21 -18
- iplotx-0.10.0/gallery/basic/plot_3d.py +29 -0
- iplotx-0.10.0/iplotx/art3d/edge.py +65 -0
- iplotx-0.10.0/iplotx/art3d/vertex.py +69 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/iplotx/artists.py +4 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/iplotx/edge/__init__.py +10 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/iplotx/edge/geometry.py +34 -1
- iplotx-0.10.0/iplotx/edge/geometry3d.py +113 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/iplotx/groups.py +19 -1
- {iplotx-0.9.0 → iplotx-0.10.0}/iplotx/ingest/providers/network/igraph.py +9 -10
- {iplotx-0.9.0 → iplotx-0.10.0}/iplotx/ingest/providers/network/networkx.py +12 -14
- {iplotx-0.9.0 → iplotx-0.10.0}/iplotx/label.py +11 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/iplotx/network.py +57 -3
- {iplotx-0.9.0 → iplotx-0.10.0}/iplotx/plotting.py +88 -41
- {iplotx-0.9.0 → iplotx-0.10.0}/iplotx/version.py +1 -1
- {iplotx-0.9.0 → iplotx-0.10.0}/iplotx/vertex.py +23 -1
- {iplotx-0.9.0 → iplotx-0.10.0}/pyproject.toml +2 -1
- iplotx-0.10.0/tests/baseline_images/test_igraph_3d/undirected.png +0 -0
- iplotx-0.10.0/tests/test_3d_mock.py +87 -0
- iplotx-0.10.0/tests/test_igraph_3d.py +40 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/uv.lock +6 -2
- {iplotx-0.9.0 → iplotx-0.10.0}/.github/workflows/publish.yml +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/.gitignore +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/.pre-commit-config.yaml +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/.readthedocs.yaml +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/LICENSE +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/MANIFEST.in +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/README.md +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/assets/pylint.svg +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/docs/Makefile +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/docs/make.bat +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/docs/source/_static/banner.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/docs/source/_static/graph_basic.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/docs/source/_templates/layout.html +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/docs/source/api/artists.md +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/docs/source/api/complete_style_specification.md +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/docs/source/api/plotting.md +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/docs/source/api/providers.md +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/docs/source/api/style.md +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/docs/source/api.md +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/docs/source/conf.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/docs/source/images/sphx_glr_plot_basic_001.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/docs/source/images/thumb/sphx_glr_plot_basic_thumb.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/docs/source/index.md +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/docs/source/providers.md +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/docs/source/style.md +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/GALLERY_HEADER.rst +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/basic/GALLERY_HEADER.rst +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/basic/plot_basic.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/basic/plot_big_curves.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/basic/plot_dag.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/basic/plot_directed.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/basic/plot_grouping.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/basic/plot_house.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/basic/plot_loops.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/basic/plot_simple_path.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/biology/GALLERY_HEADER.rst +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/biology/data/80201010000000001.mst +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/biology/data/GN-tree.json +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/biology/data/breast_cancer_string_interactions_short.tsv +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/biology/data/breast_cancer_string_network_coordinates.tsv +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/biology/data/cell_cycle_arrest_string_interactions_short.tsv +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/biology/data/cell_cycle_arrest_string_network_coordinates.tsv +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/biology/data/fevo-08-588430_DataSheet1_S1.csv +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/biology/plot_animal_phylogeny.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/biology/plot_antibody_clone.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/biology/plot_breast_cancer_ppi.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/biology/plot_cell_cycle_arrest.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/biology/plot_food_network.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/biology/plot_foraging_table.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/biology/plot_pollinators.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/biology/plot_ppi.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/biology/plot_tca_cycle.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/network_science/GALLERY_HEADER.rst +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/network_science/data/chess_masters_WCC.pgn.bz2 +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/network_science/data/knuth_miles.txt.gz +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/network_science/plot_arrowlawn.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/network_science/plot_chess_masters.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/network_science/plot_cliques.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/network_science/plot_cluster_layout.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/network_science/plot_company_structure.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/network_science/plot_complex.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/network_science/plot_financial_network.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/network_science/plot_knuth_miles.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/network_science/plot_labels_and_colors.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/network_science/plot_max_bipartite_matching.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/network_science/plot_minimum_spanning_trees.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/network_science/plot_multipartite_layout.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/network_science/plot_parallel_igraph_networkx.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/network_science/plot_redblack.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/network_science/plot_shortest_path.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/network_science/plot_simple_networkx.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/network_science/plot_social_network_circles.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/network_science/plot_traveling_salesman.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/network_science/plot_with_colorbar.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/other/GALLERY_HEADER.rst +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/other/plot_animation.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/other/plot_edit_artists.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/other/plot_feedbacks.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/other/plot_graph.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/other/plot_mouse_hover.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/other/plot_train.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/style/GALLERY_HEADER.rst +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/style/plot_arrows.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/style/plot_edgepadding.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/style/plot_elements.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/style/plot_four_grids.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/style/plot_halfarrows.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/style/plot_multistyle.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/style/plot_ports.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/style/plot_style.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/style/plot_tension.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/style/plot_vertexmarkers.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/style/plot_voronoi.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/style/plot_waypoints.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/tree/GALLERY_HEADER.rst +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/tree/data/tree-with-support.json +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/tree/plot_angular_waypoints.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/tree/plot_biopython_tree.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/tree/plot_cladeedges.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/tree/plot_cogent3_layouts.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/tree/plot_cogent3_tree.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/tree/plot_elements_tree.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/tree/plot_ete4.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/tree/plot_leafedges.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/tree/plot_leafedges_and_cascades.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/tree/plot_skbio_tree.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/tree/plot_split_edges.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/tree/plot_style_tree.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/tree/plot_support.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/tree/plot_tree_node_background.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/tree/plot_tree_style_clades.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/tree/plot_trees_of_trees.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/zero_dependency/GALLERY_HEADER.rst +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/zero_dependency/plot_simplenetworkdataprovider.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/gallery/zero_dependency/plot_simpletreedataprovider.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/iplotx/__init__.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/iplotx/cascades.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/iplotx/edge/arrow.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/iplotx/edge/leaf.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/iplotx/edge/ports.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/iplotx/ingest/__init__.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/iplotx/ingest/heuristics.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/iplotx/ingest/providers/network/simple.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/iplotx/ingest/providers/tree/biopython.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/iplotx/ingest/providers/tree/cogent3.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/iplotx/ingest/providers/tree/ete4.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/iplotx/ingest/providers/tree/simple.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/iplotx/ingest/providers/tree/skbio.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/iplotx/ingest/typing.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/iplotx/layout.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/iplotx/style/__init__.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/iplotx/style/leaf_info.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/iplotx/style/library.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/iplotx/tree.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/iplotx/typing.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/iplotx/utils/geometry.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/iplotx/utils/internal.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/iplotx/utils/matplotlib.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/iplotx/utils/style.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/scripts/copy_github_release_into_version.sh +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/scripts/make_banner.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/scripts/update_pylint_badge.sh +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_biopython/cascades.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_biopython/directed_child.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_biopython/leaf_labels.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_biopython/leaf_labels_hmargin.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_biopython/leafedges.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_biopython/show_support.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_biopython/tree_basic.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_biopython/tree_radial.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_cogent3/leaf_labels.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_cogent3/leaf_labels_hmargin.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_cogent3/tree_basic.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_cogent3/tree_radial.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_ete4/leaf_labels.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_ete4/leaf_labels_hmargin.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_ete4/split_edges.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_ete4/tree_basic.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_ete4/tree_radial.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_igraph/clustering_directed.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_igraph/clustering_directed_large.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_igraph/graph_basic.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_igraph/graph_directed.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_igraph/graph_directed_curved_loops.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_igraph/graph_edit_children.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_igraph/graph_labels.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_igraph/graph_layout_attribute.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_igraph/graph_null.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_igraph/graph_squares_directed.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_igraph/graph_vertexsize.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_igraph/graph_with_curved_edges.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_igraph/igraph_layout_object.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_igraph/multigraph_with_curved_edges_undirected.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_networkx/cluster-layout.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_networkx/complex.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_networkx/complex_rotatelabels.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_networkx/directed_graph.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_networkx/directed_graph_with_colorbar.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_networkx/empty_graph.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_networkx/flat_style.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_networkx/house_with_colors.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_networkx/labels_and_colors.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_networkx/shortest_path.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_networkx/simple_graph.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_simple_network_provider/graph_basic.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_simple_network_provider/graph_directed.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_simple_network_provider/graph_labels.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_skbio/leaf_labels.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_skbio/leaf_labels_hmargin.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_skbio/tree_basic.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/baseline_images/test_skbio/tree_radial.png +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/test_arrows.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/test_biopython.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/test_cascades.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/test_cogent3.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/test_edge.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/test_edge_geometry.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/test_ete4.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/test_geometry.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/test_heuristics.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/test_igraph.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/test_ingest_protocols.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/test_matplotlib_utils.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/test_network_hotload.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/test_networkx.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/test_ports.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/test_simple_network_provider.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/test_simple_tree_provider.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/test_skbio.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/test_style.py +0 -0
- {iplotx-0.9.0 → iplotx-0.10.0}/tests/test_vertex.py +0 -0
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"""
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3D layouts
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==========
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This example shows how to visualise graphs or networks in 3D using `iplotx`. Of course, a 3D layout is needed
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for this. Here, we use the Fruchterman-Reingold layout algorithm from ``igraph`` to generate a 3D layout.
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.. warning::
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3D visualisation does not support all features of 2D visualisation yet. Curved edges, waypoints, and labels
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are currently unsupported. PRs are welcome!
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"""
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import igraph as ig
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import iplotx as ipx
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# Make the graph
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g = ig.Graph.Erdos_Renyi(30, m=50)
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# Make a 3D layout
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layout = g.layout_fruchterman_reingold_3d()
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# Visualise the graph in 3D
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ipx.network(
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g,
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layout,
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vertex_alpha=0.7,
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edge_alpha=0.4,
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figsize=(8, 8),
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)
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"""
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Module containing code to manipulate edge visualisations in 3D, especially the Edge3DCollection class.
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"""
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from mpl_toolkits.mplot3d.art3d import (
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Line3DCollection,
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)
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from ..utils.matplotlib import (
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_forwarder,
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)
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from ..edge import (
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EdgeCollection,
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)
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@_forwarder(
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(
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"set_clip_path",
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"set_clip_box",
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"set_snap",
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"set_sketch_params",
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"set_animated",
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"set_picker",
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)
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)
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class Edge3DCollection(Line3DCollection):
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"""Collection of vertex patches for plotting."""
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pass
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def edge_collection_2d_to_3d(
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col: EdgeCollection,
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zdir: str = "z",
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depthshade: bool = True,
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axlim_clip: bool = False,
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):
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"""Convert a 2D EdgeCollection to a 3D Edge3DCollection.
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Parameters:
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zdir: The axis to use as the z axis (default is "z").
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depthshade: Whether to apply depth shading (default is True).
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axlim_clip: Whether to clip the vertices to the axes limits (default is False).
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"""
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if not isinstance(col, EdgeCollection):
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raise TypeError("vertices must be a VertexCollection")
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# TODO: if we make Edge3DCollection a dynamic drawer, this will need to change
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# fundamentally. Also, this currently does not handle labels properly.
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vinfo = col._get_adjacent_vertices_info()
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segments3d = []
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for offset1, offset2 in vinfo["offsets"]:
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segment = [tuple(offset1), tuple(offset2)]
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segments3d.append(segment)
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# NOTE: after this line, none of the EdgeCollection methods will work
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# It's become a static drawer now
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col.__class__ = Edge3DCollection
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col.set_segments(segments3d)
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col._axlim_clip = axlim_clip
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"""
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Module containing code to manipulate vertex visualisations in 3D, especially the Vertex3DCollection class.
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"""
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from typing import (
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Sequence,
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)
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import numpy as np
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from matplotlib import (
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cbook,
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)
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from mpl_toolkits.mplot3d.art3d import Path3DCollection
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from ..utils.matplotlib import (
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_forwarder,
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)
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from ..vertex import (
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VertexCollection,
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)
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@_forwarder(
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(
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"set_clip_path",
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"set_clip_box",
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"set_snap",
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"set_sketch_params",
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"set_animated",
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"set_picker",
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)
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)
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class Vertex3DCollection(VertexCollection, Path3DCollection):
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"""Collection of vertex patches for plotting."""
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def draw(self, renderer) -> None:
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"""Draw the collection of vertices in 3D.
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Parameters:
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renderer: The renderer to use for drawing.
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"""
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with self._use_zordered_offset():
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with cbook._setattr_cm(self, _in_draw=True):
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VertexCollection.draw(self, renderer)
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def vertex_collection_2d_to_3d(
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col: VertexCollection,
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zs: np.ndarray | float | Sequence[float] = 0,
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zdir: str = "z",
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axlim_clip: bool = False,
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):
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"""Convert a 2D VertexCollection to a 3D Vertex3DCollection.
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LabelCollection,
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EdgeArrowCollection,
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CascadeCollection,
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Vertex3DCollection,
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Edge3DCollection,
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@@ -193,6 +193,16 @@ class EdgeCollection(mpl.collections.PatchCollection):
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def set_transform(self, transform: mpl.transforms.Transform) -> None:
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"""
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Support module with geometry- and path-related functions for edges.
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3D geometry is in its separate module :mod:`.geometry3d`.
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"""
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)
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"""Get the coordinates of an edge tip such that it touches the vertex border.
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Parameters:
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vpath: The vertex path, in figure coordinates (so scaled by dpi).
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vsize: The vertex max size, in figure coordinates (so scaled by dpi).
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theta: The angle of the edge inpinging into the vertex, in radians, in figure coordinates.
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shrink: Additional shrinking of the edge, in figure coordinates (so scaled by dpi).
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"""
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@@ -468,7 +479,7 @@ def _compute_edge_path_curved(
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return path, tuple(thetas)
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-
def
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def _compute_edge_path_2d(
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*args,
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tension: float = 0,
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waypoints: str | tuple[float, float] | Sequence[tuple[float, float]] | np.ndarray = "none",
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@@ -502,3 +513,25 @@ def _compute_edge_path(
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ports=ports,
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**kwargs,
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)
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def _compute_edge_path(
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vcoord_data,
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*args,
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**kwargs,
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):
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+
"""Compute the edge path in either 2D or 3D.
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+
|
|
525
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+
Parameters:
|
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526
|
+
vcoord_data: The vertex coordinates in data coordinates. This is used to
|
|
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+
determine the dimensionality of the layout.
|
|
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|
+
*args: Additional arguments passed to the internal functions.
|
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|
+
**kwargs: Additional keyword arguments passed to the internal functions.
|
|
530
|
+
|
|
531
|
+
Returns:
|
|
532
|
+
The computed edge path and the angles at the start and end of the edge.
|
|
533
|
+
"""
|
|
534
|
+
ndim = len(vcoord_data[0])
|
|
535
|
+
if ndim == 2:
|
|
536
|
+
return _compute_edge_path_2d(vcoord_data, *args, **kwargs)
|
|
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|
+
return _compute_edge_path_3d(vcoord_data, *args, **kwargs)
|
|
@@ -0,0 +1,113 @@
|
|
|
1
|
+
"""
|
|
2
|
+
Support for computing edge paths in 3D.
|
|
3
|
+
"""
|
|
4
|
+
|
|
5
|
+
from typing import (
|
|
6
|
+
Optional,
|
|
7
|
+
Sequence,
|
|
8
|
+
)
|
|
9
|
+
import numpy as np
|
|
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+
import matplotlib as mpl
|
|
11
|
+
|
|
12
|
+
from ..typing import (
|
|
13
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+
Pair,
|
|
14
|
+
)
|
|
15
|
+
|
|
16
|
+
|
|
17
|
+
def _compute_edge_path_straight(
|
|
18
|
+
vcoord_data,
|
|
19
|
+
vpath_fig,
|
|
20
|
+
vsize_fig,
|
|
21
|
+
trans,
|
|
22
|
+
trans_inv,
|
|
23
|
+
layout_coordinate_system: str = "cartesian",
|
|
24
|
+
shrink: float = 0,
|
|
25
|
+
**kwargs,
|
|
26
|
+
):
|
|
27
|
+
"""Compute straight edge path between two vertices, in 3D.
|
|
28
|
+
|
|
29
|
+
Parameters:
|
|
30
|
+
vcoord_data: Vertex coordinates in data coordinates, shape (2, 3).
|
|
31
|
+
vpath_fig: Vertex path in figure coordinates.
|
|
32
|
+
vsize_fig: Vertex size in figure coordinates.
|
|
33
|
+
trans: Transformation from data to figure coordinates.
|
|
34
|
+
trans_inv: Inverse transformation from figure to data coordinates.
|
|
35
|
+
layout_coordinate_system: The coordinate system of the layout.
|
|
36
|
+
shrink: Amount to shorten the edge at each end, in figure coordinates.
|
|
37
|
+
**kwargs: Additional keyword arguments (not used).
|
|
38
|
+
Returns:
|
|
39
|
+
A pair with the path and a tuple of angles of exit and entry, in radians.
|
|
40
|
+
|
|
41
|
+
"""
|
|
42
|
+
|
|
43
|
+
if layout_coordinate_system not in ("cartesian"):
|
|
44
|
+
raise ValueError(
|
|
45
|
+
f"Layout coordinate system not supported for straight edges in 3D: {layout_coordinate_system}.",
|
|
46
|
+
)
|
|
47
|
+
|
|
48
|
+
vcoord_data_cart = vcoord_data
|
|
49
|
+
|
|
50
|
+
# Coordinates in figure (default) coords
|
|
51
|
+
vcoord_fig = trans(vcoord_data_cart)
|
|
52
|
+
|
|
53
|
+
points = []
|
|
54
|
+
|
|
55
|
+
# Angles of the straight line
|
|
56
|
+
# FIXME: In 2D, this is only used to make space for loops
|
|
57
|
+
# let's ignore for now
|
|
58
|
+
# theta = atan2(*((vcoord_fig[1] - vcoord_fig[0])[::-1]))
|
|
59
|
+
theta = 0
|
|
60
|
+
|
|
61
|
+
# TODO: Shorten at starting vertex (?)
|
|
62
|
+
vs = vcoord_fig[0]
|
|
63
|
+
points.append(vs)
|
|
64
|
+
|
|
65
|
+
# TODO: Shorten at end vertex (?)
|
|
66
|
+
ve = vcoord_fig[1]
|
|
67
|
+
points.append(ve)
|
|
68
|
+
|
|
69
|
+
codes = ["MOVETO", "LINETO"]
|
|
70
|
+
path = mpl.path.Path(
|
|
71
|
+
points,
|
|
72
|
+
codes=[getattr(mpl.path.Path, x) for x in codes],
|
|
73
|
+
)
|
|
74
|
+
path.vertices = trans_inv(path.vertices)
|
|
75
|
+
return path, (theta, theta + np.pi)
|
|
76
|
+
|
|
77
|
+
|
|
78
|
+
def _compute_edge_path_3d(
|
|
79
|
+
*args,
|
|
80
|
+
tension: float = 0,
|
|
81
|
+
waypoints: str | tuple[float, float] | Sequence[tuple[float, float]] | np.ndarray = "none",
|
|
82
|
+
ports: Pair[Optional[str]] = (None, None),
|
|
83
|
+
layout_coordinate_system: str = "cartesian",
|
|
84
|
+
**kwargs,
|
|
85
|
+
):
|
|
86
|
+
"""Compute the edge path in a few different ways."""
|
|
87
|
+
if (waypoints != "none") and (tension != 0):
|
|
88
|
+
raise ValueError("Waypoints not supported for curved edges.")
|
|
89
|
+
|
|
90
|
+
if waypoints != "none":
|
|
91
|
+
raise NotImplementedError("Waypoints not implemented for 3D edges.")
|
|
92
|
+
# return _compute_edge_path_waypoints(
|
|
93
|
+
# waypoints,
|
|
94
|
+
# *args,
|
|
95
|
+
# layout_coordinate_system=layout_coordinate_system,
|
|
96
|
+
# ports=ports,
|
|
97
|
+
# **kwargs,
|
|
98
|
+
# )
|
|
99
|
+
|
|
100
|
+
if np.isscalar(tension) and (tension == 0):
|
|
101
|
+
return _compute_edge_path_straight(
|
|
102
|
+
*args,
|
|
103
|
+
layout_coordinate_system=layout_coordinate_system,
|
|
104
|
+
**kwargs,
|
|
105
|
+
)
|
|
106
|
+
|
|
107
|
+
raise NotImplementedError("Curved edges not implemented for 3D edges.")
|
|
108
|
+
# return _compute_edge_path_curved(
|
|
109
|
+
# tension,
|
|
110
|
+
# *args,
|
|
111
|
+
# ports=ports,
|
|
112
|
+
# **kwargs,
|
|
113
|
+
# )
|
|
@@ -4,6 +4,7 @@ Module for vertex groupings code, especially the GroupingArtist class.
|
|
|
4
4
|
|
|
5
5
|
from typing import Union
|
|
6
6
|
import numpy as np
|
|
7
|
+
import pandas as pd
|
|
7
8
|
import matplotlib as mpl
|
|
8
9
|
from matplotlib.collections import PatchCollection
|
|
9
10
|
|
|
@@ -64,6 +65,9 @@ class GroupingArtist(PatchCollection):
|
|
|
64
65
|
self._points_per_curve = points_per_curve
|
|
65
66
|
|
|
66
67
|
network = kwargs.pop("network", None)
|
|
68
|
+
self.layout = normalise_layout(layout, network=network)
|
|
69
|
+
self.ndim = layout.shape[1]
|
|
70
|
+
|
|
67
71
|
patches, grouping, coords_hulls = self._create_patches(
|
|
68
72
|
grouping,
|
|
69
73
|
layout,
|
|
@@ -89,6 +93,21 @@ class GroupingArtist(PatchCollection):
|
|
|
89
93
|
self._compute_paths(self.get_figure(root=True).dpi)
|
|
90
94
|
return ret
|
|
91
95
|
|
|
96
|
+
@property
|
|
97
|
+
def axes(self):
|
|
98
|
+
return PatchCollection.axes.__get__(self)
|
|
99
|
+
|
|
100
|
+
@axes.setter
|
|
101
|
+
def axes(self, new_axes):
|
|
102
|
+
PatchCollection.axes.__set__(self, new_axes)
|
|
103
|
+
for child in self.get_children():
|
|
104
|
+
child.axes = new_axes
|
|
105
|
+
self.set_figure(new_axes.figure)
|
|
106
|
+
|
|
107
|
+
def get_layout(self) -> pd.DataFrame:
|
|
108
|
+
"""Get the layout used for this grouping."""
|
|
109
|
+
return self.layout
|
|
110
|
+
|
|
92
111
|
def get_vertexpadding(self) -> float:
|
|
93
112
|
"""Get the vertex padding of each group."""
|
|
94
113
|
return self._vertexpadding
|
|
@@ -98,7 +117,6 @@ class GroupingArtist(PatchCollection):
|
|
|
98
117
|
return self.get_vertexpadding() * dpi / 72.0 * self._factor
|
|
99
118
|
|
|
100
119
|
def _create_patches(self, grouping, layout, network, **kwargs):
|
|
101
|
-
layout = normalise_layout(layout, network=network)
|
|
102
120
|
grouping = normalise_grouping(grouping, layout)
|
|
103
121
|
style = get_style(".grouping")
|
|
104
122
|
style.pop("vertexpadding", None)
|
|
@@ -30,23 +30,22 @@ class IGraphDataProvider(NetworkDataProvider):
|
|
|
30
30
|
edge_labels: Optional[Sequence[str] | dict[str]] = None,
|
|
31
31
|
) -> NetworkData:
|
|
32
32
|
"""Create network data object for iplotx from an igraph object."""
|
|
33
|
-
network = self.network
|
|
34
|
-
directed = self.is_directed()
|
|
35
33
|
|
|
36
|
-
#
|
|
37
|
-
if np.isscalar(vertex_labels) and (not vertex_labels):
|
|
38
|
-
vertex_labels = None
|
|
39
|
-
|
|
40
|
-
# Vertices are ordered integers, no gaps
|
|
34
|
+
# Get layout
|
|
41
35
|
vertex_df = normalise_layout(
|
|
42
36
|
layout,
|
|
43
|
-
network=network,
|
|
37
|
+
network=self.network,
|
|
44
38
|
nvertices=self.number_of_vertices(),
|
|
45
39
|
)
|
|
46
40
|
ndim = vertex_df.shape[1]
|
|
47
41
|
vertex_df.columns = _make_layout_columns(ndim)
|
|
48
42
|
|
|
43
|
+
# Vertices are ordered integers, no gaps
|
|
44
|
+
|
|
49
45
|
# Vertex labels
|
|
46
|
+
# Recast vertex_labels=False as vertex_labels=None
|
|
47
|
+
if np.isscalar(vertex_labels) and (not vertex_labels):
|
|
48
|
+
vertex_labels = None
|
|
50
49
|
if vertex_labels is not None:
|
|
51
50
|
if np.isscalar(vertex_labels):
|
|
52
51
|
vertex_df["label"] = vertex_df.index.astype(str)
|
|
@@ -57,7 +56,7 @@ class IGraphDataProvider(NetworkDataProvider):
|
|
|
57
56
|
|
|
58
57
|
# Edges are a list of tuples, because of multiedges
|
|
59
58
|
tmp = []
|
|
60
|
-
for edge in network.es:
|
|
59
|
+
for edge in self.network.es:
|
|
61
60
|
row = {"_ipx_source": edge.source, "_ipx_target": edge.target}
|
|
62
61
|
row.update(edge.attributes())
|
|
63
62
|
tmp.append(row)
|
|
@@ -76,7 +75,7 @@ class IGraphDataProvider(NetworkDataProvider):
|
|
|
76
75
|
network_data = {
|
|
77
76
|
"vertex_df": vertex_df,
|
|
78
77
|
"edge_df": edge_df,
|
|
79
|
-
"directed":
|
|
78
|
+
"directed": self.is_directed(),
|
|
80
79
|
"ndim": ndim,
|
|
81
80
|
}
|
|
82
81
|
return network_data
|
|
@@ -33,25 +33,20 @@ class NetworkXDataProvider(NetworkDataProvider):
|
|
|
33
33
|
|
|
34
34
|
import networkx as nx
|
|
35
35
|
|
|
36
|
-
|
|
37
|
-
|
|
38
|
-
directed = self.is_directed()
|
|
39
|
-
|
|
40
|
-
# Recast vertex_labels=False as vertex_labels=None
|
|
41
|
-
if np.isscalar(vertex_labels) and (not vertex_labels):
|
|
42
|
-
vertex_labels = None
|
|
43
|
-
|
|
44
|
-
# Vertices are indexed by node ID
|
|
36
|
+
# Get layout
|
|
45
37
|
vertex_df = normalise_layout(
|
|
46
38
|
layout,
|
|
47
|
-
network=network,
|
|
39
|
+
network=self.network,
|
|
48
40
|
nvertices=self.number_of_vertices(),
|
|
49
|
-
)
|
|
41
|
+
)
|
|
50
42
|
ndim = vertex_df.shape[1]
|
|
51
43
|
vertex_df.columns = _make_layout_columns(ndim)
|
|
52
44
|
|
|
45
|
+
# Vertices are indexed by node ID
|
|
46
|
+
vertex_df = vertex_df.loc[pd.Index(self.network.nodes)]
|
|
47
|
+
|
|
53
48
|
# Vertex internal properties
|
|
54
|
-
tmp = pd.DataFrame(dict(network.nodes.data())).T
|
|
49
|
+
tmp = pd.DataFrame(dict(self.network.nodes.data())).T
|
|
55
50
|
# Arrays become a single column, which we have already anyway
|
|
56
51
|
if isinstance(layout, str) and (layout in tmp.columns):
|
|
57
52
|
del tmp[layout]
|
|
@@ -60,6 +55,9 @@ class NetworkXDataProvider(NetworkDataProvider):
|
|
|
60
55
|
del tmp
|
|
61
56
|
|
|
62
57
|
# Vertex labels
|
|
58
|
+
# Recast vertex_labels=False as vertex_labels=None
|
|
59
|
+
if np.isscalar(vertex_labels) and (not vertex_labels):
|
|
60
|
+
vertex_labels = None
|
|
63
61
|
if vertex_labels is None:
|
|
64
62
|
if "label" in vertex_df:
|
|
65
63
|
del vertex_df["label"]
|
|
@@ -78,7 +76,7 @@ class NetworkXDataProvider(NetworkDataProvider):
|
|
|
78
76
|
|
|
79
77
|
# Edges are a list of tuples, because of multiedges
|
|
80
78
|
tmp = []
|
|
81
|
-
for u, v, d in network.edges.data():
|
|
79
|
+
for u, v, d in self.network.edges.data():
|
|
82
80
|
row = {"_ipx_source": u, "_ipx_target": v}
|
|
83
81
|
row.update(d)
|
|
84
82
|
tmp.append(row)
|
|
@@ -112,7 +110,7 @@ class NetworkXDataProvider(NetworkDataProvider):
|
|
|
112
110
|
network_data = {
|
|
113
111
|
"vertex_df": vertex_df,
|
|
114
112
|
"edge_df": edge_df,
|
|
115
|
-
"directed":
|
|
113
|
+
"directed": self.is_directed(),
|
|
116
114
|
"ndim": ndim,
|
|
117
115
|
}
|
|
118
116
|
return network_data
|
|
@@ -77,6 +77,17 @@ class LabelCollection(mpl.artist.Artist):
|
|
|
77
77
|
child.set_figure(fig)
|
|
78
78
|
self._update_offsets(dpi=fig.dpi)
|
|
79
79
|
|
|
80
|
+
def set_transform(self, transform: mpl.transforms.Transform) -> None:
|
|
81
|
+
"""Set the transform for this artist and children.
|
|
82
|
+
|
|
83
|
+
Parameters:
|
|
84
|
+
transform: The transform to set.
|
|
85
|
+
"""
|
|
86
|
+
super().set_transform(transform)
|
|
87
|
+
if hasattr(self, "_labelartists"):
|
|
88
|
+
for art in self._labelartists:
|
|
89
|
+
art.set_transform(transform)
|
|
90
|
+
|
|
80
91
|
def get_texts(self):
|
|
81
92
|
"""Get the texts of the labels."""
|
|
82
93
|
return [child.get_text() for child in self.get_children()]
|