Man pages for jmw86069/jamenrich
Analysis and Visualization of Multiple Gene Set Enrichments
| add_pathway_direction | Add directionality to pathway enrichment |
| adjust_cnet_nodeset | Adjust Cnet node set |
| adjust_cnet_set_relayout_gene | Adjust Set nodes then relayout Gene nodes |
| adjust_polygon_border | Adjust polygon border to inner or outer edge |
| apply_cnet_direction | Apply Cnet border color by directionality |
| apply_nodeset_spacing | Apply minimum node spacing for each Cnet node set |
| avg_angles | Average geometric angles |
| avg_colors_by_list | Average colors by list |
| call_fn_ellipsis_deprecated | Call function using safe ellipsis arguments |
| cell_fun_bivariate | ComplexHeatmap cell function with bivariant color |
| cnet2df | Summarize Cnet igraph as a data.frame |
| cnet2im | Convert Cnet igraph to incidence matrix |
| cnetplot_internalJam | cnetplot internal function |
| cnetplotJam | Create a cnetplot igraph object |
| collapse_mem_clusters | Collapse Multienrichment clusters |
| color_edges_by_nodegroups | Color edges by nodegroups |
| color_edges_by_nodes | Colorize igraph edges by nodes |
| color_edges_by_nodes_deprecated | Color igraph edges using node colors (deprecated) |
| color_nodes_by_nodegroups | Color edges by nodegroups |
| colorRamp2D | Color ramp for bivariate colors |
| colors_from_list | Ordered colors from a list of color vectors |
| communities2nodegroups | Convert communities object to nodegroups list format |
| curateIPAcolnames | Curate Ingenuity IPA colnames |
| deconcat_df2 | Deconcatenate delimited column values in a data.frame |
| default_igraph_values | Default igraph parameter values |
| display_colorRamp2D | Display colors from bivariate color function |
| drawEllipse | Draw ellipse |
| edge_bundle_bipartite | Bundle edges in a bipartite graph |
| edge_bundle_nodegroups | Bundle edges using node groups |
| enrichDF2enrichResult | Convert data.frame to enrichResult |
| enrichList2df | Convert enrichList to data.frame |
| enrichList2geneHitList | Extract gene hit list from list of enrichResult |
| enrichList2IM | Convert enrichList to IM incidence matrix |
| enrichMapJam | Create enrichMap igraph object |
| filter_mem_genes | Filter mem multienrichment object by Gene names |
| filter_mem_sets | Filter mem multienrichment object by Set names |
| find_colname | Find colname by character string or pattern matching |
| fixSetLabels | Fix Set labels for legibility |
| flip_edges | Flip direction of igraph edges |
| get_bipartite_nodeset | Get partite/connected graph nodesets |
| get_cnet_nodeset | Get Cnet node set by connected Sets |
| get_hull_data | Get data for alpha hull (internal) |
| get_igraph_arrow_mode | Get igraph arrow mode |
| get_igraph_layout | Obtain or create layout for igraph object |
| grid_with_title | Draw Heatmap with title and subtitle using grid viewports |
| gsubs_remove | Pattern replacement with multiple patterns |
| handle_igraph_param_list | Handle igraph attribute parameter list |
| heatmap_column_order_deprecated | Return Heatmap column order |
| heatmap_row_order_deprecated | Return Heatmap row order (deprecated) |
| igraph2pieGraph | Convert igraph to use pie node shapes |
| im2list | convert incidence matrix to list |
| im2list_dep | convert incidence matrix to list |
| importIPAenrichment | Import Ingenuity IPA enrichment results |
| imSigned2list | convert signed incidence matrix to list |
| imSigned2list_dep | convert signed incidence matrix to list |
| isColorBlank | Determine if colors are blank colors |
| jam_igraph | Jam wrapper to plot igraph |
| jam_igraph_arrows | Render igraph arrows |
| jam_mypie | Vectorized mypie() function for igraph vertex pie polygons |
| jam_plot_igraph | Jam igraph vectorized plot function (internal) |
| label_communities | Assign labels to igraph communities |
| layout_with_qfr | igraph layout using qgraph Fruchterman-Reingold |
| layout_with_qfrf | igraph layout function using qgraph Fruchterman-Reingold |
| list2concordance | Convert list to concordance matrix |
| list2im | convert list to incidence matrix |
| list2imSigned | convert list to signeddirectional incidence matrix |
| make_cnet_test | Make Cnet test igraph |
| make_legend_bivariate | Display colors from bivariate color function |
| make_point_hull | Make alpha hull from points |
| mem2emap | Convert multiEnrichMap mem output to EnrichmentMap emap |
| mem_enrichment_heatmap | MultiEnrichment Heatmap of enrichment P-values |
| mem_find_overlap | Find best overlap threshold for EnrichMap |
| mem_gene_path_heatmap | MultiEnrichment Heatmap of Genes and Pathways |
| memIM2cnet | Convert MultiEnrichment incidence matrix to Cnet plot |
| mem_legend | MultiEnrichMap color legend |
| mem_multienrichplot | MultiEnrichMap plot |
| mem_plot_folio | Multienrichment folio of summary plots |
| multiEnrichMap | Prepare MultiEnrichMap data from enrichList |
| nodegroups2communities | Convert nodegroups list to communities object |
| nudge_igraph_node | Nudge igraph layout by node |
| order_colors | Order colors |
| parse_igraph_plot_params | Parse igraph plot params |
| plot_layout_scale | Plot layout scale by percentage of coordinate range |
| rank_mem_clusters | Rank Multienrichment clusters |
| rectifyPiegraph | Convert pie igraph node shapes to coloredrectangle |
| relayout_with_qfr | igraph re-layout using qgraph Fruchterman-Reingold |
| removeIgraphBlanks | Remove igraph blank wedges |
| removeIgraphSinglets | Remove igraph singlet nodes |
| reorderIgraphNodes | Re-order igraph nodes |
| rotate_coordinates | Rotate numeric coordinates |
| rotate_igraph_layout | Rotate igraph layout coordinates |
| shape.coloredrectangle.plot | custom igraph vertex shape coloredrectangle |
| shape.ellipse.clip | clip function for igraph vertex shape ellipse |
| shape.ellipse.plot | plot function for igraph vertex shape ellipse |
| shape.jampie.plot | custom igraph vertex shape jampie |
| sort_colors_deprecated | Sort colors (deprecated) |
| spread_igraph_labels | Spread igraph node labels by angle from node center |
| subgraph_jam | Subgraph using Jam extended logic |
| subsetCnetIgraph | Subset Cnet igraph |
| subset_igraph_components | Subset igraph by connected components |
| subset_mem | Subset mem multienrichment object |
| summarize_node_spacing | Summarize spacing between igraph nodes given a layout |
| sync_igraph_communities | Sync igraph nodes and communities |
| topEnrichBySource | Subset enrichResult for top enrichment results by source |
| with_qfr | Layout specification for Qgraph Fruchterman-Reingold |
| xyAngle | Get angle from origin to vector of x,y coordinates |
