├── README.md ├── bioRxiv ├── LICENSE ├── Linked.png ├── README.md ├── gold.png ├── jp_gene_viz.bib ├── jp_gene_viz.pdf ├── jp_gene_viz.tex ├── motif.png ├── old_linked.png └── pair.png ├── doc ├── Combined widgets.ipynb ├── Setting up a network from scratch and specifying colors, sizes, etcetera.ipynb ├── dNetwork widget overview.ipynb ├── dNetwork_settings.png ├── heat_map_widget.png ├── multiple_network.png └── network.png ├── environment.yml ├── examples ├── Diagram using cytoscape with js_proxy.ipynb ├── Directory explorer using Highcharts with js_proxy.ipynb ├── Heat map.ipynb ├── HighCharts using js_proxy.ipynb ├── LAS_fit.py ├── Linked Heatmap and Network.ipynb ├── Miscellaneous examples.ipynb ├── Motif widget usage.ipynb ├── Multiple Coordinated Networks.ipynb ├── Network Pair.ipynb ├── Network with line styles.ipynb ├── Network.ipynb ├── Todo list using js_proxy.ipynb ├── chrX.wig.gz ├── color test.ipynb ├── cytoscape demo.ipynb ├── ex2.wig.gz ├── examine interactive data structure example.ipynb ├── expr.tsv ├── genes.gtf ├── js_proxy example.ipynb ├── mm9_em.meme ├── network.tsv ├── network.tsv.layout.json ├── network2.tsv ├── network2.tsv.layout.json ├── network_styled.tsv └── three.js using js_proxy.ipynb ├── experiments ├── Breast cancer nearest neighbor classification.ipynb ├── Compositional Geometry.ipynb ├── Inverse CLR.ipynb ├── Iris.ipynb ├── README.md ├── compositional.py ├── graph diagram test.ipynb ├── graph.data ├── nearest_neighbors.py ├── nn3d.py ├── p.zip ├── static 3d iris neareast neighbors.ipynb └── three widget examples.ipynb ├── index.ipynb ├── jp_gene_viz ├── FontUtils.js ├── HMap.py ├── LAS_fit.py ├── LExpression.py ├── OrbitControls.js ├── TextGeometry.js ├── __init__.py ├── addenda.py ├── array_transforms.py ├── bindings.py ├── category_layout.py ├── cluster_layout.py ├── color_cursor.js ├── color_scale.py ├── color_widget.py ├── cytoscape.js ├── dExpression.py ├── dGraph.py ├── dLayout.py ├── dNetwork.py ├── doodle3d.py ├── encrypt_files.py ├── examine.py ├── file_chooser_widget.py ├── fs_chart.py ├── genome_bar.py ├── genome_guide.py ├── genome_wiggle.py ├── getData.py ├── graph_diagram.py ├── grid_forest.py ├── gtf_format.py ├── helvetiker_regular.typeface.js ├── jp_cytoscape.js ├── jp_cytoscape.py ├── js_context.py ├── js_proxy.js ├── js_proxy.py ├── json_mixin.py ├── morph_triangles.js ├── motif_data.py ├── multiple_network.py ├── paired_links.py ├── paired_networks.py ├── proxy_html5_canvas.py ├── scale.py ├── scatter3d.py ├── sequence_motifs.js ├── server_file_chooser.js ├── simple_tree.py ├── simple_upload_button.js ├── spoke_layout.py ├── test │ ├── __init__.py │ ├── test_HMap.py │ ├── test_array_transforms.py │ ├── test_color_scale.py │ ├── test_fit.py │ ├── test_jp_cytoscape.py │ ├── test_motif.py │ └── test_wig.py ├── three.js ├── three_curve.js ├── three_orbit.js ├── three_rotator.js ├── three_scatter.js ├── three_simple_text.js ├── three_sprite_text.js ├── three_triangles.js └── 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