Files in cograph

Analysis and Visualization of Complex Networks

NEWS.md README.md R/cograph-package.R R/aes-nodes.R R/sonplot-qgraph-geometry.R R/utils-validation.R R/layout-groups.R R/plot-mcml.R R/plot-nestimate.R R/plot-bootstrap.R R/render-nodes.R R/splot-geometry.R R/layout-spring.R R/aaa-globals.R R/from-qgraph.R R/shapes-basic.R R/input-edgelist.R R/network-summary.R R/plot-simplicial.R R/input-matrix.R R/palettes.R R/splot-arrows.R R/network-utils.R R/input-tna.R R/input-parse.R R/methods-print.R R/class-network.R R/cluster-metrics.R R/shapes-special.R R/utils-colors.R R/data-hai.R R/tplot.R R/plot-chord.R R/motifs-plot.R R/motifs.R R/motifs-api.R R/methods-plot.R R/splot.R R/blob-helpers.R R/splot-labels.R R/communities.R R/aes-scales.R R/centrality.R R/simplify.R R/mlna.R R/render-edges.R R/splot-polygons.R R/plot-heatmap.R R/motifs-extract.R R/splot-params.R R/plot-communities.R R/layout-registry.R R/utils-globals.R R/themes-registry.R R/layout-gephi-fr.R R/data-student-interactions.R R/render-grid.R R/plot-transitions.R R/output-save.R R/cograph.R R/shapes-svg.R R/robustness.R R/plot-forest.R R/motifs-data.R R/plot-htna.R R/shapes-registry.R R/themes-builtin.R R/layout-circle.R R/render-ggplot.R R/class-layout.R R/splot-edges.R R/plot-htna-multi.R R/utils-geometry.R R/splot-nodes.R R/zzz.R R/class-theme.R R/disparity.R R/input-igraph.R R/input-qgraph.R R/scale-constants.R R/plot-mixed-network.R R/utils-deprecation.R R/input-statnet.R R/plot-compare.R R/aes-edges.R R/plot-ml-heatmap.R R/layout-oval.R R/plot-permutation.R inst/doc/input-formats.R inst/doc/input-formats.Rmd inst/doc/introduction.R inst/doc/introduction.Rmd tests/testthat.R tests/testthat/test-plot-simplicial.R tests/testthat/test-coverage-render-nodes-40.R tests/testthat/test-coverage-utils-deprecation-41.R tests/testthat/test-plot-chord.R tests/testthat/test-splot.R tests/testthat/test-coverage-tplot-40.R tests/testthat/test-coverage-plot-permutation-40.R tests/testthat/test-coverage-plot-transitions-41.R tests/testthat/test-coverage-input-igraph-42.R tests/testthat/test-layout-spring-animation.R tests/testthat/test-coverage-100pct.R tests/testthat/test-plot-forest.R tests/testthat/test-coverage-themes-registry-40.R tests/testthat/test-coverage-utils-colors-41.R tests/testthat/test-coverage-mlna-40.R tests/testthat/test-coverage-render-grid-41.R tests/testthat/test-coverage-utils-validation-41.R tests/testthat/test-edge-cases.R tests/testthat/helper-test-utils.R tests/testthat/test-coverage-layout-registry-41.R tests/testthat/test-cograph.R tests/testthat/test-tna-temporal.R tests/testthat/test-disparity.R tests/testthat/test-coverage-input-qgraph-41.R tests/testthat/test-coverage-shapes-registry-40.R tests/testthat/test-palettes.R tests/testthat/test-sn-nodes.R tests/testthat/test-coverage-cluster-metrics-40.R tests/testthat/test-coverage-layout-circle-41.R tests/testthat/test-themes.R tests/testthat/test-coverage-round7.R tests/testthat/test-coverage-plot-compare-40.R tests/testthat/test-coverage-100pct-v2.R tests/testthat/test-coverage-plot-htna-40.R tests/testthat/test-coverage-scale-constants-43.R tests/testthat/test-coverage-splot-labels-40.R tests/testthat/test-coverage-cluster-metrics-41.R tests/testthat/test-coverage-aes-nodes-42.R tests/testthat/test-coverage-utils-geometry-43.R tests/testthat/test-coverage-shapes-registry-41.R tests/testthat/test-coverage-shapes-svg-41.R tests/testthat/test-coverage-plot-htna-multi-41.R tests/testthat/test-coverage-splot-geometry-40.R tests/testthat/test-coverage-plot-mcml-41.R tests/testthat/test-coverage-layout-registry-40.R tests/testthat/test-coverage-splot-arrows-40.R tests/testthat/test-coverage-plot-hon-40.R tests/testthat/test-coverage-render-grid-40.R tests/testthat/test-coverage-layout-oval-40.R tests/testthat/test-coverage-methods-print-42.R tests/testthat/test-coverage-cograph-41.R tests/testthat/test-coverage-input-statnet-41.R tests/testthat/test-coverage-input-tna-40.R tests/testthat/test-overlay-communities.R tests/testthat/test-coverage-plot-ml-heatmap-41.R tests/testthat/test-layouts.R tests/testthat/test-coverage-themes-registry-41.R tests/testthat/test-coverage-motifs-44.R tests/testthat/test-layouts-extended.R tests/testthat/test-coverage-render-grid-42.R tests/testthat/test-coverage-plot-heatmap-40.R tests/testthat/test-themes-extended.R tests/testthat/test-coverage-class-network-41.R tests/testthat/test-coverage-plot-mcml-42.R tests/testthat/test-coverage-layout-groups-42.R tests/testthat/test-coverage-motifs-43.R tests/testthat/test-coverage-motifs-40.R tests/testthat/test-validate-nestimate-bootstrap-permutation.R tests/testthat/test-coverage-plot-mcml-40.R tests/testthat/test-qgraph-args.R tests/testthat/test-coverage-cograph-40.R tests/testthat/test-coverage-100pct-final.R tests/testthat/test-coverage-layout-spring-40.R tests/testthat/test-coverage-splot-41.R tests/testthat/test-coverage-network-utils-40.R tests/testthat/test-from-converters.R tests/testthat/test-coverage-plot-nestimate-40.R tests/testthat/test-coverage-mlna-41.R tests/testthat/test-coverage-splot-params-41.R tests/testthat/test-motifs-equivalence.R tests/testthat/test-coverage-splot-polygons-41.R tests/testthat/test-coverage-network-summary-40.R tests/testthat/test-plot-compare.R tests/testthat/test-coverage-plot-htna-41.R tests/testthat/test-plot-mixed-network.R tests/testthat/test-coverage-sonplot-qgraph-geometry-41.R tests/testthat/test-coverage-layout-groups-41.R tests/testthat/test-coverage-plot-htna-multi-40.R tests/testthat/test-coverage-network-utils-42.R tests/testthat/test-coverage-splot-42.R tests/testthat/test-shapes.R tests/testthat/test-coverage-layout-gephi-fr-40.R tests/testthat/test-coverage-input-igraph-41.R tests/testthat/test-coverage-plot-bootstrap-40.R tests/testthat/test-coverage-motifs-41.R tests/testthat/test-coverage-class-network-40.R tests/testthat/test-coverage-methods-print-40.R tests/testthat/test-ggplot.R tests/testthat/test-tna-integration.R tests/testthat/test-coverage-output-save-43.R tests/testthat/test-coverage-aes-edges-41.R tests/testthat/test-coverage-input-parse-40.R tests/testthat/test-coverage-render-edges-41.R tests/testthat/test-coverage-zzz-41.R tests/testthat/test-coverage-round6.R tests/testthat/test-coverage-output-save-41.R tests/testthat/test-coverage-communities-41.R tests/testthat/test-robustness.R tests/testthat/test-centrality.R tests/testthat/test-coverage-splot-nodes-40.R tests/testthat/test-coverage-methods-plot-42.R tests/testthat/test-cluster-metrics.R tests/testthat/test-sn-edges.R tests/testthat/test-coverage-class-layout-40.R tests/testthat/test-network-summary.R tests/testthat/helper-cograph.R tests/testthat/test-integration.R tests/testthat/test-motifs-api.R tests/testthat/test-coverage-round5.R tests/testthat/test-input-parse.R tests/testthat/test-coverage-render-nodes-41.R tests/testthat/test-coverage-palettes-40.R tests/testthat/test-sn-save.R tests/testthat/test-soplot.R tests/testthat/test-coverage-plot-ml-heatmap-40.R tests/testthat/test-coverage-communities-40.R tests/testthat/test-simplify.R tests/testthat/test-build-mcml.R tests/testthat/test-coverage-from-qgraph-40.R tests/testthat/test-coverage-splot-edges-40.R tests/testthat/test-coverage-centrality-40.R vignettes/input-formats.Rmd vignettes/introduction.Rmd vignettes/articles/comparison-plots-demo.Rmd vignettes/articles/function-reference.Rmd vignettes/articles/mcml-examples.Rmd vignettes/articles/plotting-tna-models.Rmd vignettes/articles/why-cograph.Rmd vignettes/articles/network-structure-and-groups.Rmd man/dot-create_cograph_network.Rd man/sn_ggplot.Rd man/centrality_eigenvector.Rd man/dot-plot_compare_all_pairs.Rd man/select_nodes.Rd man/render_legend_grid.Rd man/dot-draw_intra_group_edges.Rd man/plot-permutation.Rd man/compute_connectivity_jitter_vertical.Rd man/dot-heatmap_theme.Rd man/expand_param.Rd man/resolve_stars.Rd man/map_qgraph_shape.Rd man/get_template_from_style.Rd man/arrow_base_midpoint.Rd man/compute_connectivity_jitter_horizontal.Rd man/draw_self_loop_base.Rd man/sn_save.Rd man/rescale_layout.Rd man/get_layout.Rd man/supra_adjacency.Rd man/plot-heatmap.Rd man/community_walktrap.Rd man/tna_color_palette.Rd man/create_edges_df.Rd man/centrality_current_flow_betweenness.Rd man/plot_edge_diff_forest.Rd man/plot_htna.Rd man/dot-build_ml_shells.Rd man/draw_network_node_base.Rd man/is_directed.Rd man/get_theme.Rd man/plot_group_permutation.Rd man/dot-build_ml_cells.Rd man/draw_double_donut_pie_node_base.Rd man/plot.cograph_communities.Rd man/splot-edges.Rd man/resolve_edge_labels.Rd man/usr_to_in_x.Rd man/plot-bootstrap.Rd man/register_theme.Rd man/unregister_svg_shape.Rd man/compute_circular_layout.Rd man/filter_edges_by_weight.Rd man/hexagon_vertices.Rd man/list_layouts.Rd man/circle_vertices.Rd man/themes-builtin.Rd man/draw_robot_node_base.Rd man/layout_spring.Rd man/qgraph_cent_to_edge_simple.Rd man/centrality_transitivity.Rd man/recycle_to_length.Rd man/layout_circle.Rd man/verify_with_igraph.Rd man/create_nodes_df.Rd man/get_y_scale.Rd man/in_to_usr_x.Rd man/compute_adaptive_esize.Rd man/parse_svg.Rd man/draw_database_node_base.Rd man/centrality_strength.Rd man/dot-resolve_colors.Rd man/draw_square.Rd man/theme_cograph_colorblind.Rd man/draw_self_loop.Rd man/render_legend_splot.Rd man/bezier_points.Rd man/to_data_frame.Rd man/as_tna.Rd man/render-grid.Rd man/cograph.Rd man/sn_palette.Rd man/dot-transform_to_plane.Rd man/dot-process_weights.Rd man/get_shape_vertices.Rd man/dot-resolve_weights.Rd man/set_edges.Rd man/build_edge_labels_from_template.Rd man/print.cograph_communities.Rd man/theme_cograph_classic.Rd man/methods-plot.Rd man/validate_choice.Rd man/robustness.Rd man/draw_diamond.Rd man/draw_open_arrow_base.Rd man/diamond_vertices.Rd man/validate_network.Rd man/to_network.Rd man/plot_simplicial.Rd man/motif_census.Rd man/validate_color.Rd man/map_qgraph_lty.Rd man/draw_pentagon.Rd man/resolve_loop_rotation.Rd man/draw_gear.Rd man/centrality_pagerank.Rd man/is_cograph_theme.Rd man/scale_size.Rd man/network_cut_vertices.Rd man/qgraph_cent2edge.Rd man/validate_length.Rd man/splot-geometry.Rd man/aes-scales.Rd man/dot-wrap_communities.Rd man/set_nodes.Rd man/dot-normalize_clusters.Rd man/nodes.Rd man/network_radius.Rd man/sn_save_ggplot.Rd man/draw_pie.Rd man/network_bridges.Rd man/extract_motifs.Rd man/fontface_to_string.Rd man/dot-extract_weights.Rd man/sn_nodes.Rd man/square_vertices.Rd man/network_clique_size.Rd man/utils-deprecation.Rd man/cluster_summary.Rd man/palette_colorblind.Rd man/select_neighbors.Rd man/scale_edge_widths.Rd man/centrality_laplacian.Rd man/communities.Rd man/draw_neural.Rd man/register_builtin_themes.Rd man/draw_polygon_donut_pie_node_base.Rd man/compute_polygon_layout.Rd man/dot-plot_heatmap_clustered.Rd man/aes-nodes.Rd man/zzz.Rd man/shorten_edge_for_arrow.Rd man/utils-globals.Rd man/splot-arrows.Rd man/render_nodes_splot.Rd man/centrality_voterank.Rd man/get_edges.Rd man/network_rich_club.Rd man/centrality_leverage.Rd man/get_labels.Rd man/get_edge_list.Rd man/draw_edge_label_base.Rd man/point_angle.Rd man/centrality_coreness.Rd man/layout-groups.Rd man/plot-compare.Rd man/plot_netobject_ml.Rd man/handle_deprecated_param.Rd man/draw_network.Rd man/centrality_power.Rd man/qgraph_arrow_size.Rd man/inset_polygon_vertices.Rd man/plot_heatmap.Rd man/splot-params.Rd man/shapes-basic.Rd man/draw_curved_edge_base.Rd man/select_bridges.Rd man/community_label_propagation.Rd man/dot-build_cluster_lookup.Rd man/theme_cograph_minimal.Rd man/detect_communities.Rd man/community_edge_betweenness.Rd man/palette_rainbow.Rd man/splot-nodes.Rd man/robustness_auc.Rd man/filter_nodes.Rd man/overlay_communities.Rd man/create_grid_grob.Rd man/draw_curved_edge.Rd man/regular_polygon_vertices.Rd man/set_groups.Rd man/get_data.Rd man/layout_oval.Rd man/in_to_usr_y.Rd man/compare_communities.Rd man/curve_control_point.Rd man/dot-decode_tna_data.Rd man/dot-auto_detect_clusters.Rd man/triad_census.Rd man/resolve_edge_widths.Rd man/layout-circle.Rd man/COGRAPH_SCALE.Rd man/plot_tna.Rd man/CographNetwork.Rd man/shapes-svg.Rd man/centrality_diffusion.Rd man/build_mcml.Rd man/select_top_edges.Rd man/input-igraph.Rd man/resolve_donut_params.Rd man/atan2_usr.Rd man/get_svg_shape.Rd man/draw_circle_arrow_base.Rd man/render_edges_splot.Rd man/community_optimal.Rd man/arrow_radius.Rd man/layout_gephi_fr.Rd man/cluster_quality.Rd man/register_builtin_palettes.Rd man/qgraph_default_vsize.Rd man/ellipse_vertices.Rd man/dot-as_mcml.Rd man/pentagon_vertices.Rd man/plot.cograph_motifs.Rd man/sn_theme.Rd man/dot-translate_qgraph_dots.Rd man/draw_robot.Rd man/QGRAPH_SCALE.Rd man/heart_vertices.Rd man/degree_distribution.Rd man/dot-tna_style_defaults.Rd man/get_edge_label_position.Rd man/print.cograph_network.Rd man/network_summary.Rd man/palettes.Rd man/compute_edge_curvatures.Rd man/aggregate_duplicate_edges.Rd man/palette_reds.Rd man/plot_chord.Rd man/is_symmetric_matrix.Rd man/sn_edges.Rd man/dot-add_cluster_borders.Rd man/to_matrix.Rd man/centrality_closeness.Rd man/check_duplicate_edges.Rd man/supra_interlayer.Rd man/splot.net_bootstrap.Rd man/robustness_summary.Rd man/hai_datasets.Rd man/render_node_labels_grid.Rd man/dot-plot_heatmap_single.Rd man/as_mcml.Rd man/plot_alluvial.Rd man/plot-transitions.Rd man/star_vertices.Rd man/dot-add_heatmap_values.Rd man/is_cograph_network.Rd man/render_nodes_grid.Rd man/CographLayout.Rd man/qgraph_vsize_to_user.Rd man/input-parse.Rd man/draw_triangle.Rd man/filter_edges.Rd man/dot-compute_modularity.Rd man/splot.Rd man/n_nodes.Rd man/register_builtin_shapes.Rd man/centrality_load.Rd man/summary.cograph_network.Rd man/dot-extract_inits.Rd man/palette_pastel.Rd man/mcml.Rd man/layout-spring.Rd man/input-tna.Rd man/cograph-main.Rd man/supra_layer.Rd man/cograph-package.Rd man/resolve_edge_styles.Rd man/draw_chip.Rd man/get_significance_stars.Rd man/theme_cograph_viridis.Rd man/from_qgraph.Rd man/list_svg_shapes.Rd man/layout-oval.Rd man/color_communities.Rd man/dot-build_ml_labels.Rd man/scale_color.Rd man/network_local_efficiency.Rd man/community_consensus.Rd man/draw_node_base.Rd man/scale_color_discrete.Rd man/simplify.Rd man/dot-extract_ml_layers.Rd man/cloud_vertices.Rd man/resolve_edge_colors.Rd man/render_edges_base.Rd man/splot_angle.Rd man/get_x_scale.Rd man/sn_layout.Rd man/community_fast_greedy.Rd man/qgraph_norm_curve.Rd man/select_edges.Rd man/scale_alpha.Rd man/plot_mixed_network.Rd man/scale_edge_widths_simple.Rd man/format_pvalue.Rd man/utils-validation.Rd man/register_svg_shape.Rd man/draw_ellipse.Rd man/theme_cograph_dark.Rd man/draw_star.Rd man/resolve_node_colors.Rd man/plot_bootstrap_forest.Rd man/draw_circle.Rd man/plot-nestimate.Rd man/centrality_percolation.Rd man/plot.cograph_cluster_significance.Rd man/draw_node_label_base.Rd man/plot_mlna.Rd man/set_layout.Rd man/scale-constants.Rd man/themes-registry.Rd man/plot_netobject_group.Rd man/list_shapes.Rd man/arrow_head_points.Rd man/splot.netobject.Rd man/draw_double_donut_pie.Rd man/CographTheme.Rd man/draw_hexagon.Rd man/network_small_world.Rd man/modularity.cograph_communities.Rd man/utils-colors.Rd man/shapes-special.Rd man/robustness_edge_attack.Rd man/input-matrix.Rd man/plot.cograph_motif_analysis.Rd man/layer_similarity_matrix.Rd man/centrality_betweenness.Rd man/centrality_authority.Rd man/plot.cograph_network.Rd man/format_ci_range.Rd man/palette_blues.Rd man/draw_svg_shape_base.Rd man/resolve_shapes.Rd man/draw_cross.Rd man/offset_point.Rd man/get_donut_base_vertices.Rd man/select_component.Rd man/find_curve_split_index.Rd man/init_registries.Rd man/brain_vertices.Rd man/network_global_efficiency.Rd man/render_edge_labels_grid.Rd man/theme_cograph_gray.Rd man/draw_arrow_base.Rd man/palette_diverging.Rd man/qgraph_default_esize.Rd man/to_igraph.Rd man/network_vertex_connectivity.Rd man/student_interactions.Rd man/plot_mcml.Rd man/methods-print.Rd man/community_spinglass.Rd man/extract_triads.Rd man/layer_degree_correlation.Rd man/point_distance.Rd man/dot-build_ml_connections.Rd man/select_top.Rd man/splot.tna_disparity.Rd man/aes-edges.Rd man/draw_cloud.Rd man/draw_heart.Rd man/community_sizes.Rd man/parse_input.Rd man/get_edge_order.Rd man/draw_svg_shape.Rd man/centrality_degree.Rd man/dot-add_cluster_labels.Rd man/render_nodes_base.Rd man/layout_groups.Rd man/plot_robustness.Rd man/robustness_vertex_attack.Rd man/point_on_circle.Rd man/plot_comparison_heatmap.Rd man/cent_to_edge.Rd man/ggplot_robustness.Rd man/aggregate_layers.Rd man/disparity.Rd man/draw_brain.Rd man/splot.wtna_mixed.Rd man/membership.cograph_communities.Rd man/is_tna_network.Rd man/perp_mid.Rd man/get_source.Rd man/globals.Rd man/community_leading_eigenvector.Rd man/fontface_to_numeric.Rd man/centrality_constraint.Rd man/draw_polygon_donut.Rd man/resolve_aesthetic.Rd man/qgraph_plot_info.Rd man/community_louvain.Rd man/input-qgraph.Rd man/centrality_harmonic.Rd man/rectangle_vertices.Rd man/draw_donut_node_base.Rd man/centrality.Rd man/draw_donut_pie_node_base.Rd man/gear_vertices.Rd man/centrality_kreach.Rd man/render-edges.Rd man/plot_mtna.Rd man/draw_curve_with_start_segment.Rd man/cluster_significance.Rd man/community_fluid.Rd man/resolve_label_sizes.Rd man/get_nodes.Rd man/network_girth.Rd man/theme_cograph_nature.Rd man/soplot.Rd man/draw_pie_node_base.Rd man/compute_plot_limits.Rd man/register_layout.Rd man/qgraph_scale_edge_widths.Rd man/plot_compare.Rd man/COGRAPH_SCALE_LEGACY.Rd man/abbrev_label.Rd man/dot-disparity_filter_matrix.Rd man/dot-build_mcml_sequence.Rd man/select_edges_between.Rd man/resolve_node_sizes.Rd man/draw_neural_node_base.Rd man/get_scale_constants.Rd man/scale_node_sizes.Rd man/plot_ml_heatmap.Rd man/detect_duplicate_edges.Rd man/map_edge_colors.Rd man/dot-matrix_to_long.Rd man/edge_centrality.Rd man/layer_similarity.Rd man/draw_database.Rd man/register_shape.Rd man/render_edges_grid.Rd man/utils-geometry.Rd man/palette_viridis.Rd man/aggregate_weights.Rd man/layout-registry.Rd man/plot_permutation.Rd man/splot.net_permutation.Rd man/get_node_order.Rd man/draw_donut_pie.Rd man/resolve_centrality_sizes.Rd man/format_edge_label_template.Rd man/splot-polygons.Rd man/n_communities.Rd man/get_shape.Rd man/register_builtin_layouts.Rd man/map_node_colors.Rd man/validate_range.Rd man/list_palettes.Rd man/splot-labels.Rd man/summarize_network.Rd man/plot.tna_disparity.Rd man/draw_curved_arrow_base.Rd man/output-save.Rd man/dot-group_tna_to_mcml.Rd man/centrality_alpha.Rd man/compute_layout_gephi_fr.Rd man/draw_straight_edge.Rd man/sonplot-qgraph-geometry.Rd man/disparity_filter.Rd man/cross_vertices.Rd man/render-ggplot.Rd man/dot-build_heatmap_base.Rd man/centrality_current_flow_closeness.Rd man/edge_endpoint.Rd man/dot-detect_mcml_input.Rd man/n_edges.Rd man/dot-draw_intra_arc.Rd man/get_meta.Rd man/from_tna.Rd man/subgraphs.Rd man/as_cograph.Rd man/draw_donut.Rd man/usr_to_in_y.Rd man/centrality_eccentricity.Rd man/dot-build_from_transitions.Rd man/render-nodes.Rd man/draw_chip_node_base.Rd man/splot.boot_glasso.Rd man/community_leiden.Rd man/arrow_points.Rd man/list_themes.Rd man/resolve_labels.Rd man/dot-build_mcml_edgelist.Rd man/scale_width.Rd man/get_groups.Rd man/motifs.Rd man/dot-plot_heatmap_group_tna.Rd man/draw_straight_edge_base.Rd man/shapes-registry.Rd man/select_edges_involving.Rd man/dot-resolve_ml_colors.Rd man/input-statnet.Rd man/plot_transitions.Rd man/draw_polygon_donut_node_base.Rd man/plot_trajectories.Rd man/triangle_vertices.Rd man/input-edgelist.Rd man/community_infomap.Rd man/centrality_subgraph.Rd man/splot.tna_bootstrap.Rd