├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── AllClasses.R ├── AllGenerics.R ├── jam-ashape.R ├── jam-deconcat.R ├── jam-igraph-internals.R ├── jam-igraph-plot.R ├── jam-points-to-ahull.R ├── jam-polygon-borders.R ├── jamenrich-apply-cnet-direction.R ├── jamenrich-apply-cnet-spacing.R ├── jamenrich-base.r ├── jamenrich-bivariatecolor.R ├── jamenrich-bulk-cnet-adjustments.R ├── jamenrich-cnet.R ├── jamenrich-color-nodes-edges.R ├── jamenrich-communities-nodegroups.R ├── jamenrich-direction.R ├── jamenrich-enrichdf2er.R ├── jamenrich-enrichlist2df.R ├── jamenrich-find-enrich-colnames.R ├── jamenrich-fix-set-labels.R ├── jamenrich-get-igraph-layout.R ├── jamenrich-get-mem.R ├── jamenrich-handle-rowcol-splits.R ├── jamenrich-highlights.R ├── jamenrich-igraph.r ├── jamenrich-igraphshapes.R ├── jamenrich-import.R ├── jamenrich-jam-plot-igraph.R ├── jamenrich-make-cnet-test.R ├── jamenrich-mem-plot-folio.R ├── jamenrich-mem2cnet.R ├── jamenrich-mem2emap.R ├── jamenrich-plot.R ├── jamenrich-rotate.R ├── jamenrich-score-gene-path-clusters.R ├── jamenrich-sets.r ├── jamenrich-summarize-node-spacing.R ├── jamenrich-topenrich.R ├── jamenrich-utils.R ├── jamenrich-with-ht-opts.R ├── jamgraph-edgebundle.R ├── jamgraph-relayout-nodegroups.R ├── methods-Mem.R ├── methods-MemPlotFolio.R ├── multienrichjam-data.R ├── multienrichjam-package.R ├── shinycat-server.R ├── shinycat-ui-launch.R ├── sysdata.rda └── zzz.R ├── README.Rmd ├── README.md ├── TODO.md ├── _pkgdown.yml ├── data-raw └── update_data.R ├── data ├── Memtest.rda ├── Reese_genes.rda ├── abbrev.rda ├── msig_test.rda └── words.rda ├── docs ├── 404.html ├── LICENSE-text.html ├── LICENSE.html ├── TODO.html ├── TODO_freshenGenes.html ├── articles │ ├── MemPlotConcepts.html │ ├── importClusterProfiler.html │ ├── importClusterProfiler_files │ │ ├── figure-html │ │ │ ├── cnet-cluster-1.png │ │ │ ├── cnet-collapsed-1.png │ │ │ ├── mem-folio-1.png │ │ │ ├── mem-folio-2.png │ │ │ ├── mem-folio-3.png │ │ │ └── mem-folio-4.png │ │ ├── kePrint-0.0.1 │ │ │ └── kePrint.js │ │ └── lightable-0.0.1 │ │ │ └── lightable.css │ ├── importIPA.html │ ├── importIPA_files │ │ ├── accessible-code-block-0.0.1 │ │ │ └── empty-anchor.js │ │ ├── figure-html │ │ │ ├── cnet-cluster-1.png │ │ │ ├── cnet-collapsed-1.png │ │ │ ├── cnet-plot-1-1.png │ │ │ ├── cnet-plot-1-custom-1.png │ │ │ ├── cnet-plot-2-1.png │ │ │ ├── enrich-hm-1-1.png │ │ │ ├── enrich-hm-1.png │ │ │ ├── enrich-hm-2-1.png │ │ │ ├── enrich-hm-2-2.png │ │ │ ├── enrich-hm-mpf-1.png │ │ │ ├── jam-igraph-1-1.png │ │ │ ├── jam-igraph-2-1.png │ │ │ ├── mem-folio-1.png │ │ │ ├── mem-folio-2.png │ │ │ ├── mem-folio-3.png │ │ │ ├── mem-folio-4.png │ │ │ ├── mem-hm-1.png │ │ │ ├── mem-hm-mpf-1.png │ │ │ ├── mem-plot-1-1.png │ │ │ ├── mem-plot-1b-1.png │ │ │ ├── mem-plot-2-1.png │ │ │ ├── subnet-1.png │ │ │ └── subnet2-1.png │ │ ├── header-attrs-2.1 │ │ │ └── header-attrs.js │ │ ├── header-attrs-2.9 │ │ │ └── header-attrs.js │ │ ├── kePrint-0.0.1 │ │ │ └── kePrint.js │ │ └── lightable-0.0.1 │ │ │ └── lightable.css │ ├── index.html │ └── shinycat-2.png ├── authors.html ├── bootstrap-toc.css ├── bootstrap-toc.js ├── cnet_heatmap_guide.html ├── deps │ ├── bootstrap-5.3.1 │ │ ├── bootstrap.bundle.min.js │ │ ├── bootstrap.bundle.min.js.map │ │ ├── bootstrap.min.css │ │ ├── font.css │ │ └── fonts │ │ │ ├── 07d40e985ad7c747025dabb9f22142c4.woff2 │ │ │ ├── 1Ptug8zYS_SKggPNyC0ITw.woff2 │ │ │ ├── 1Ptug8zYS_SKggPNyCAIT5lu.woff2 │ │ │ ├── 1Ptug8zYS_SKggPNyCIIT5lu.woff2 │ │ │ ├── 1Ptug8zYS_SKggPNyCMIT5lu.woff2 │ │ │ ├── 1Ptug8zYS_SKggPNyCkIT5lu.woff2 │ │ │ ├── 1f5e011d6aae0d98fc0518e1a303e99a.woff2 │ │ │ ├── 4iCs6KVjbNBYlgoKcQ72j00.woff2 │ │ │ ├── 4iCs6KVjbNBYlgoKcg72j00.woff2 │ │ │ ├── 4iCs6KVjbNBYlgoKcw72j00.woff2 │ │ │ ├── 4iCs6KVjbNBYlgoKew72j00.woff2 │ │ │ ├── 4iCs6KVjbNBYlgoKfA72j00.woff2 │ │ │ ├── 4iCs6KVjbNBYlgoKfw72.woff2 │ │ │ ├── 4iCv6KVjbNBYlgoCxCvjs2yNL4U.woff2 │ │ │ ├── 4iCv6KVjbNBYlgoCxCvjsGyN.woff2 │ │ │ ├── 4iCv6KVjbNBYlgoCxCvjtGyNL4U.woff2 │ │ │ ├── 4iCv6KVjbNBYlgoCxCvjvGyNL4U.woff2 │ │ │ ├── 4iCv6KVjbNBYlgoCxCvjvWyNL4U.woff2 │ │ │ ├── 4iCv6KVjbNBYlgoCxCvjvmyNL4U.woff2 │ │ │ ├── 626330658504e338ee86aec8e957426b.woff2 │ │ │ ├── 6xK1dSBYKcSV-LCoeQqfX1RYOo3qPZ7jsDJT9g.woff2 │ │ │ ├── 6xK1dSBYKcSV-LCoeQqfX1RYOo3qPZ7ksDJT9g.woff2 │ │ │ ├── 6xK1dSBYKcSV-LCoeQqfX1RYOo3qPZ7nsDI.woff2 │ │ │ ├── 6xK1dSBYKcSV-LCoeQqfX1RYOo3qPZ7osDJT9g.woff2 │ │ │ ├── 6xK1dSBYKcSV-LCoeQqfX1RYOo3qPZ7psDJT9g.woff2 │ │ │ ├── 6xK1dSBYKcSV-LCoeQqfX1RYOo3qPZ7qsDJT9g.woff2 │ │ │ ├── 6xK1dSBYKcSV-LCoeQqfX1RYOo3qPZ7rsDJT9g.woff2 │ │ │ ├── 6xK3dSBYKcSV-LCoeQqfX1RYOo3qN67lqDY.woff2 │ │ │ ├── 6xK3dSBYKcSV-LCoeQqfX1RYOo3qNK7lqDY.woff2 │ │ │ ├── 6xK3dSBYKcSV-LCoeQqfX1RYOo3qNa7lqDY.woff2 │ │ │ ├── 6xK3dSBYKcSV-LCoeQqfX1RYOo3qNq7lqDY.woff2 │ │ │ ├── 6xK3dSBYKcSV-LCoeQqfX1RYOo3qO67lqDY.woff2 │ │ │ ├── 6xK3dSBYKcSV-LCoeQqfX1RYOo3qOK7l.woff2 │ │ │ ├── 6xK3dSBYKcSV-LCoeQqfX1RYOo3qPK7lqDY.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3i54rwkxduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3i54rwlBduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3i54rwlxdu.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3i54rwmBduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3i54rwmRduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3i54rwmhduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3i54rwmxduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwkxduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwlBduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwlxdu.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwmBduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwmRduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwmhduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwmxduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwkxduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwlBduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwlxdu.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwmBduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwmRduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwmhduz8A.woff2 │ │ │ ├── 6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwmxduz8A.woff2 │ │ │ ├── CSR54z1Qlv-GDxkbKVQ_dFsvWNReuQ.woff2 │ │ │ ├── CSR54z1Qlv-GDxkbKVQ_dFsvWNpeudwk.woff2 │ │ │ ├── CSR64z1Qlv-GDxkbKVQ_fO4KTet_.woff2 │ │ │ ├── CSR64z1Qlv-GDxkbKVQ_fOAKTQ.woff2 │ │ │ ├── HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvQlMIXxw.woff2 │ │ │ ├── HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvUlMI.woff2 │ │ │ ├── HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvXlMIXxw.woff2 │ │ │ ├── HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvYlMIXxw.woff2 │ │ │ ├── HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvZlMIXxw.woff2 │ │ │ ├── HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvalMIXxw.woff2 │ │ │ ├── HI_QiYsKILxRpg3hIP6sJ7fM7PqlONvblMIXxw.woff2 │ │ │ ├── HI_SiYsKILxRpg3hIP6sJ7fM7PqlM-vWjMY.woff2 │ │ │ ├── HI_SiYsKILxRpg3hIP6sJ7fM7PqlMOvWjMY.woff2 │ │ │ ├── HI_SiYsKILxRpg3hIP6sJ7fM7PqlMevWjMY.woff2 │ │ │ ├── HI_SiYsKILxRpg3hIP6sJ7fM7PqlMuvWjMY.woff2 │ │ │ ├── HI_SiYsKILxRpg3hIP6sJ7fM7PqlOevWjMY.woff2 │ │ │ ├── HI_SiYsKILxRpg3hIP6sJ7fM7PqlPevW.woff2 │ │ │ ├── HI_SiYsKILxRpg3hIP6sJ7fM7PqlPuvWjMY.woff2 │ │ │ ├── JTUSjIg1_i6t8kCHKm459W1hyzbi.woff2 │ │ │ ├── JTUSjIg1_i6t8kCHKm459WRhyzbi.woff2 │ │ │ ├── JTUSjIg1_i6t8kCHKm459WZhyzbi.woff2 │ │ │ ├── JTUSjIg1_i6t8kCHKm459Wdhyzbi.woff2 │ │ │ ├── JTUSjIg1_i6t8kCHKm459Wlhyw.woff2 │ │ │ ├── QGYpz_kZZAGCONcK2A4bGOj8mNhN.woff2 │ │ │ ├── S6u8w4BMUTPHjxsAUi-qJCY.woff2 │ │ │ ├── S6u8w4BMUTPHjxsAXC-q.woff2 │ │ │ ├── S6u9w4BMUTPHh6UVSwaPGR_p.woff2 │ │ │ ├── S6u9w4BMUTPHh6UVSwiPGQ.woff2 │ │ │ ├── S6u9w4BMUTPHh7USSwaPGR_p.woff2 │ │ │ ├── S6u9w4BMUTPHh7USSwiPGQ.woff2 │ │ │ ├── S6uyw4BMUTPHjx4wXg.woff2 │ │ │ ├── S6uyw4BMUTPHjxAwXjeu.woff2 │ │ │ ├── XRXV3I6Li01BKofIMeaBXso.woff2 │ │ │ ├── XRXV3I6Li01BKofINeaB.woff2 │ │ │ ├── XRXV3I6Li01BKofIO-aBXso.woff2 │ │ │ ├── XRXV3I6Li01BKofIOOaBXso.woff2 │ │ │ ├── XRXV3I6Li01BKofIOuaBXso.woff2 │ │ │ ├── c2f002b3a87d3f9bfeebb23d32cfd9f8.woff2 │ │ │ ├── ee91700cdbf7ce16c054c2bb8946c736.woff2 │ │ │ ├── memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqW106F15M.woff2 │ │ │ ├── memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWt06F15M.woff2 │ │ │ ├── memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWtE6F15M.woff2 │ │ │ ├── memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWtU6F15M.woff2 │ │ │ ├── memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWtk6F15M.woff2 │ │ │ ├── memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWu06F15M.woff2 │ │ │ ├── memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWuU6F.woff2 │ │ │ ├── memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWuk6F15M.woff2 │ │ │ ├── memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWvU6F15M.woff2 │ │ │ ├── memtYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWqWxU6F15M.woff2 │ │ │ ├── memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTS-muw.woff2 │ │ │ ├── memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTS2mu1aB.woff2 │ │ │ ├── memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSCmu1aB.woff2 │ │ │ ├── memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSGmu1aB.woff2 │ │ │ ├── memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSKmu1aB.woff2 │ │ │ ├── memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSOmu1aB.woff2 │ │ │ ├── memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSumu1aB.woff2 │ │ │ ├── memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTSymu1aB.woff2 │ │ │ ├── memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTUGmu1aB.woff2 │ │ │ ├── memvYaGs126MiZpBA-UvWbX2vVnXBbObj2OVTVOmu1aB.woff2 │ │ │ ├── q5uGsou0JOdh94bfuQltOxU.woff2 │ │ │ └── q5uGsou0JOdh94bfvQlt.woff2 │ ├── bootstrap-toc-1.0.1 │ │ └── bootstrap-toc.min.js │ ├── clipboard.js-2.0.11 │ │ └── clipboard.min.js │ ├── data-deps.txt │ ├── font-awesome-6.5.2 │ │ ├── css │ │ │ ├── all.css │ │ │ ├── all.min.css │ │ │ ├── v4-shims.css │ │ │ └── v4-shims.min.css │ │ └── webfonts │ │ │ ├── fa-brands-400.ttf │ │ │ ├── fa-brands-400.woff2 │ │ │ ├── fa-regular-400.ttf │ │ │ ├── fa-regular-400.woff2 │ │ │ ├── fa-solid-900.ttf │ │ │ ├── fa-solid-900.woff2 │ │ │ ├── fa-v4compatibility.ttf │ │ │ └── fa-v4compatibility.woff2 │ ├── headroom-0.11.0 │ │ ├── headroom.min.js │ │ └── jQuery.headroom.min.js │ ├── jquery-3.6.0 │ │ ├── jquery-3.6.0.js │ │ ├── jquery-3.6.0.min.js │ │ └── jquery-3.6.0.min.map │ └── search-1.0.0 │ │ ├── autocomplete.jquery.min.js │ │ ├── fuse.min.js │ │ └── mark.min.js ├── docsearch.css ├── docsearch.js ├── index.html ├── katex-auto.js ├── lightswitch.js ├── link.svg ├── mem_function_notes.html ├── mem_vignettes.html ├── multienrichjam_dev_notes.html ├── multienrichjam_workflow_notes.html ├── news │ └── index.html ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml ├── reference │ ├── Caption,MemPlotFolio-method.html │ ├── CaptionLegendList,MemPlotFolio-method.html │ ├── Clusters,MemPlotFolio-method.html │ ├── CnetCluster,MemPlotFolio-method.html │ ├── CnetCollapsed,MemPlotFolio-method.html │ ├── CnetExemplar,MemPlotFolio-method.html │ ├── EnrichmentHeatmap,MemPlotFolio-method.html │ ├── GeneClusters,MemPlotFolio-method.html │ ├── GenePathHeatmap,MemPlotFolio-method.html │ ├── IPAlist_to_hits.html │ ├── Mem-class.html │ ├── Mem-data.html │ ├── Mem-methods.html │ ├── Mem-slots.html │ ├── Mem.html │ ├── MemPlotFolio-class-1.png │ ├── MemPlotFolio-class-2.png │ ├── MemPlotFolio-class-3.png │ ├── MemPlotFolio-class-4.png │ ├── MemPlotFolio-class-5.png │ ├── MemPlotFolio-class.html │ ├── MemPlotFolio.html │ ├── MemPlotFolio_to_list.html │ ├── Mem_to_list.html │ ├── Memtest.html │ ├── Reese_genes.html │ ├── Rplot001.png │ ├── Rplot002.png │ ├── Rplot003.png │ ├── Rplot004.png │ ├── Rplot005.png │ ├── Rplot006.png │ ├── Rplot007.png │ ├── Rplot008.png │ ├── Rplot009.png │ ├── Rplot010.png │ ├── [,Mem,ANY,ANY,ANY-method.html │ ├── abbrev.html │ ├── add_pathway_direction.html │ ├── adjust_cnet_nodeset.html │ ├── adjust_cnet_set_relayout_gene.html │ ├── adjust_polygon_border-1.png │ ├── adjust_polygon_border-2.png │ ├── adjust_polygon_border-3.png │ ├── adjust_polygon_border-4.png │ ├── adjust_polygon_border-5.png │ ├── adjust_polygon_border.html │ ├── adjust_rect_border.html │ ├── apply_cnet_direction.html │ ├── apply_color_cap.html │ ├── apply_nodeset_spacing.html │ ├── as.html │ ├── as.list,Mem-method.html │ ├── ashape-1.png │ ├── ashape.html │ ├── avg_angles.html │ ├── avg_colors_by_list-1.png │ ├── avg_colors_by_list-2.png │ ├── avg_colors_by_list.html │ ├── bulk_cnet_adjustments.html │ ├── cell_fun_bivariate-1.png │ ├── cell_fun_bivariate-2.png │ ├── cell_fun_bivariate-3.png │ ├── cell_fun_bivariate-4.png │ ├── cell_fun_bivariate.html │ ├── check_Mem.html │ ├── check_MemPlotFolio.html │ ├── cnet2df.html │ ├── cnet2im.html │ ├── cnetplotJam.html │ ├── cnetplot_internalJam.html │ ├── coerce.html │ ├── collapse_mem_clusters.html │ ├── colorRamp2D-1.png │ ├── colorRamp2D-2.png │ ├── colorRamp2D-3.png │ ├── colorRamp2D-4.png │ ├── colorRamp2D-5.png │ ├── colorRamp2D.html │ ├── colorV,Mem-method.html │ ├── color_edges_by_nodegroups.html │ ├── color_edges_by_nodes.html │ ├── color_edges_by_nodes_deprecated.html │ ├── color_nodes_by_nodegroups.html │ ├── colors_from_list.html │ ├── communities2nodegroups.html │ ├── curateIPAcolnames.html │ ├── deconcat_df2.html │ ├── default_igraph_values.html │ ├── dim,Mem-method.html │ ├── dimnames,Mem-method.html │ ├── display_colorRamp2D.html │ ├── drawEllipse-1.png │ ├── drawEllipse.html │ ├── edge_bundle_bipartite.html │ ├── edge_bundle_nodegroups-1.png │ ├── edge_bundle_nodegroups.html │ ├── enrichDF2enrichResult.html │ ├── enrichIM,Mem-method.html │ ├── enrichIMcolors,Mem-method.html │ ├── enrichIMdirection,Mem-method.html │ ├── enrichIMgeneCount,Mem-method.html │ ├── enrichList,Mem-method.html │ ├── enrichList2IM.html │ ├── enrichList2df.html │ ├── enrichList2geneHitList.html │ ├── enrichMapJam.html │ ├── enrichments,Mem-method.html │ ├── figures │ │ ├── README-cnet-cluster-1.png │ │ ├── README-cnet-collapsed-1.png │ │ ├── README-cnet-collapsed-set-1.png │ │ ├── README-cnet-exemplar-1.png │ │ ├── README-cnet-exemplar-custom-1.png │ │ ├── README-enrichment-heatmap-1.png │ │ └── README-gp-heatmap-1.png │ ├── filter_mem_genes.html │ ├── filter_mem_sets.html │ ├── find_colname.html │ ├── find_enrich_colnames.html │ ├── fixSetLabels-1.png │ ├── fixSetLabels.html │ ├── flip_edges-1.png │ ├── flip_edges-2.png │ ├── flip_edges.html │ ├── geneHitIM,Mem-method.html │ ├── geneHitList,Mem-method.html │ ├── geneIM,Mem-method.html │ ├── geneIMcolors,Mem-method.html │ ├── geneIMdirection,Mem-method.html │ ├── geneInCategory,Mem-method.html │ ├── genes,Mem-method.html │ ├── get_bipartite_nodeset.html │ ├── get_cnet_nodeset.html │ ├── get_cnet_nodeset_vector.html │ ├── get_hull_data.html │ ├── get_igraph_arrow_mode.html │ ├── get_igraph_layout-1.png │ ├── get_igraph_layout-2.png │ ├── get_igraph_layout-3.png │ ├── get_igraph_layout.html │ ├── grid_with_title.html │ ├── gsubs.html │ ├── gsubs_remove.html │ ├── handle_igraph_param_list.html │ ├── handle_rowcol_splits.html │ ├── headers,Mem-method.html │ ├── heatmap_column_order.html │ ├── heatmap_column_order_deprecated.html │ ├── heatmap_row_order.html │ ├── heatmap_row_order_deprecated.html │ ├── highlight_edges_by_node-1.png │ ├── highlight_edges_by_node-2.png │ ├── highlight_edges_by_node-3.png │ ├── highlight_edges_by_node.html │ ├── igraph2pieGraph.html │ ├── im2list.html │ ├── im2list_dep.html │ ├── imSigned2list.html │ ├── imSigned2list_dep.html │ ├── importIPAenrichment.html │ ├── index.html │ ├── isColorBlank.html │ ├── jam_igraph-1.png │ ├── jam_igraph-10.png │ ├── jam_igraph-2.png │ ├── jam_igraph-3.png │ ├── jam_igraph-4.png │ ├── jam_igraph-5.png │ ├── jam_igraph-6.png │ ├── jam_igraph-7.png │ ├── jam_igraph-8.png │ ├── jam_igraph-9.png │ ├── jam_igraph.html │ ├── jam_igraph_arrows-1.png │ ├── jam_igraph_arrows.html │ ├── jam_mypie.html │ ├── jam_plot_igraph.html │ ├── label_communities.html │ ├── launch_shinycat.html │ ├── layout_with_qfr-1.png │ ├── layout_with_qfr.html │ ├── layout_with_qfrf.html │ ├── list2concordance.html │ ├── list2im.html │ ├── list2imSigned.html │ ├── list_to_Mem.html │ ├── list_to_MemPlotFolio.html │ ├── local_ht_opts.html │ ├── make_cnet_test-1.png │ ├── make_cnet_test-2.png │ ├── make_cnet_test-3.png │ ├── make_cnet_test-4.png │ ├── make_cnet_test-5.png │ ├── make_cnet_test-6.png │ ├── make_cnet_test-7.png │ ├── make_cnet_test-8.png │ ├── make_cnet_test-9.png │ ├── make_cnet_test.html │ ├── make_legend_bivariate-1.png │ ├── make_legend_bivariate-2.png │ ├── make_legend_bivariate-3.png │ ├── make_legend_bivariate-4.png │ ├── make_legend_bivariate-5.png │ ├── make_legend_bivariate.html │ ├── make_point_hull-1.png │ ├── make_point_hull-2.png │ ├── make_point_hull-3.png │ ├── make_point_hull-4.png │ ├── make_point_hull.html │ ├── mem2cnet-1.png │ ├── mem2cnet.html │ ├── mem2emap.html │ ├── memIM,Mem-method.html │ ├── memIM2cnet.html │ ├── mem_enrichment_heatmap.html │ ├── mem_find_overlap.html │ ├── mem_gene_path_heatmap.html │ ├── mem_legend.html │ ├── mem_multienrichplot.html │ ├── mem_plot_folio-1.png │ ├── mem_plot_folio-2.png │ ├── mem_plot_folio-3.png │ ├── mem_plot_folio-4.png │ ├── mem_plot_folio.html │ ├── mergeAllXY.html │ ├── metadata,MemPlotFolio-method.html │ ├── multiEnrichMap.html │ ├── multienrichjam-package.html │ ├── multienrichjam.html │ ├── names,Mem-method.html │ ├── nodegroups2communities.html │ ├── nudge_igraph_node.html │ ├── order_colors-1.png │ ├── order_colors.html │ ├── parse_igraph_plot_params.html │ ├── plot_layout_scale.html │ ├── prepare_folio.html │ ├── rank_mem_clusters.html │ ├── rectifyPiegraph.html │ ├── relayout_nodegroups-1.png │ ├── relayout_nodegroups-2.png │ ├── relayout_nodegroups-3.png │ ├── relayout_nodegroups.html │ ├── relayout_with_qfr.html │ ├── removeIgraphBlanks-1.png │ ├── removeIgraphBlanks-2.png │ ├── removeIgraphBlanks.html │ ├── removeIgraphSinglets.html │ ├── reorderIgraphNodes-1.png │ ├── reorderIgraphNodes-2.png │ ├── reorderIgraphNodes-3.png │ ├── reorderIgraphNodes-4.png │ ├── reorderIgraphNodes-5.png │ ├── reorderIgraphNodes-6.png │ ├── reorderIgraphNodes-7.png │ ├── reorderIgraphNodes.html │ ├── reorder_igraph_nodes.html │ ├── rotate_coordinates-1.png │ ├── rotate_coordinates.html │ ├── rotate_igraph_layout-1.png │ ├── rotate_igraph_layout-2.png │ ├── rotate_igraph_layout.html │ ├── score_gene_path_clusters-1.png │ ├── score_gene_path_clusters-2.png │ ├── score_gene_path_clusters.html │ ├── set_igraph_layout.html │ ├── sets,Mem-method.html │ ├── setsByGene,Mem-method.html │ ├── shape.coloredrectangle.clip.html │ ├── shape.coloredrectangle.plot-1.png │ ├── shape.coloredrectangle.plot-2.png │ ├── shape.coloredrectangle.plot-3.png │ ├── shape.coloredrectangle.plot.html │ ├── shape.ellipse.clip.html │ ├── shape.ellipse.plot.html │ ├── shape.jampie.clip.html │ ├── shape.jampie.plot-1.png │ ├── shape.jampie.plot-2.png │ ├── shape.jampie.plot-3.png │ ├── shape.jampie.plot-4.png │ ├── shape.jampie.plot.html │ ├── shinycat_server.html │ ├── shinycat_ui.html │ ├── show,Mem-method.html │ ├── show,MemPlotFolio-method.html │ ├── some_vector.html │ ├── sort_colors-1.png │ ├── sort_colors-2.png │ ├── sort_colors-3.png │ ├── sort_colors.html │ ├── sort_colors_deprecated-1.png │ ├── sort_colors_deprecated-2.png │ ├── sort_colors_deprecated-3.png │ ├── sort_colors_deprecated.html │ ├── spread_igraph_labels.html │ ├── subgraph_jam.html │ ├── subsetCnetIgraph.html │ ├── subset_igraph_components.html │ ├── subset_mem.html │ ├── summarize_node_spacing-1.png │ ├── summarize_node_spacing.html │ ├── sync_igraph_communities.html │ ├── thresholds,Mem-method.html │ ├── thresholds,MemPlotFolio-method.html │ ├── topEnrichBySource.html │ ├── topEnrichListBySource.html │ ├── unnestList.html │ ├── updateObject,Mem-method.html │ ├── with_ht_opts.html │ ├── with_qfr.html │ ├── words.html │ └── xyAngle.html ├── search.json └── sitemap.xml ├── inst ├── CITATION └── extdata │ ├── Newborns-IPA.txt │ ├── OlderChildren-IPA.txt │ ├── abbrev.txt │ └── words.txt ├── man ├── IPAlist_to_hits.Rd ├── Mem-class.Rd ├── Mem-data.Rd ├── Mem-slots.Rd ├── MemPlotFolio-class.Rd ├── add_pathway_direction.Rd ├── adjust_cnet_nodeset.Rd ├── adjust_cnet_set_relayout_gene.Rd ├── adjust_polygon_border.Rd ├── apply_cnet_direction.Rd ├── apply_nodeset_spacing.Rd ├── ashape.Rd ├── avg_angles.Rd ├── avg_colors_by_list.Rd ├── bulk_cnet_adjustments.Rd ├── cell_fun_bivariate.Rd ├── check_Mem.Rd ├── check_MemPlotFolio.Rd ├── cnet2df.Rd ├── cnet2im.Rd ├── cnetplotJam.Rd ├── collapse_mem_clusters.Rd ├── colorRamp2D.Rd ├── color_edges_by_nodegroups.Rd ├── color_edges_by_nodes.Rd ├── color_nodes_by_nodegroups.Rd ├── colors_from_list.Rd ├── communities2nodegroups.Rd ├── curateIPAcolnames.Rd ├── deconcat_df2.Rd ├── default_igraph_values.Rd ├── display_colorRamp2D.Rd ├── drawEllipse.Rd ├── edge_bundle_bipartite.Rd ├── edge_bundle_nodegroups.Rd ├── enrichDF2enrichResult.Rd ├── enrichList2IM.Rd ├── enrichList2df.Rd ├── enrichList2geneHitList.Rd ├── enrichMapJam.Rd ├── figures │ ├── README-cnet-cluster-1.png │ ├── README-cnet-collapsed-1.png │ ├── README-cnet-collapsed-set-1.png │ ├── README-cnet-exemplar-1.png │ ├── README-cnet-exemplar-custom-1.png │ ├── README-enrichment-heatmap-1.png │ └── README-gp-heatmap-1.png ├── find_colname.Rd ├── find_enrich_colnames.Rd ├── fixSetLabels.Rd ├── flip_edges.Rd ├── get_bipartite_nodeset.Rd ├── get_cnet_nodeset.Rd ├── get_cnet_nodeset_vector.Rd ├── get_hull_data.Rd ├── get_igraph_arrow_mode.Rd ├── get_igraph_layout.Rd ├── grid_with_title.Rd ├── gsubs_remove.Rd ├── handle_igraph_param_list.Rd ├── handle_rowcol_splits.Rd ├── highlight_edges_by_node.Rd ├── igraph2pieGraph.Rd ├── im2list.Rd ├── imSigned2list.Rd ├── importIPAenrichment.Rd ├── isColorBlank.Rd ├── jam_igraph.Rd ├── jam_igraph_arrows.Rd ├── jam_mypie.Rd ├── jam_plot_igraph.Rd ├── label_communities.Rd ├── launch_shinycat.Rd ├── layout_with_qfr.Rd ├── layout_with_qfrf.Rd ├── list2concordance.Rd ├── list2im.Rd ├── list2imSigned.Rd ├── make_cnet_test.Rd ├── make_legend_bivariate.Rd ├── make_point_hull.Rd ├── mem2cnet.Rd ├── mem2emap.Rd ├── mem_enrichment_heatmap.Rd ├── mem_find_overlap.Rd ├── mem_gene_path_heatmap.Rd ├── mem_legend.Rd ├── mem_multienrichplot.Rd ├── mem_plot_folio.Rd ├── multiEnrichMap.Rd ├── multienrichjam-package.Rd ├── nodegroups2communities.Rd ├── nudge_igraph_node.Rd ├── order_colors.Rd ├── plot_layout_scale.Rd ├── rank_mem_clusters.Rd ├── rectifyPiegraph.Rd ├── relayout_nodegroups.Rd ├── relayout_with_qfr.Rd ├── removeIgraphBlanks.Rd ├── removeIgraphSinglets.Rd ├── reorderIgraphNodes.Rd ├── rotate_coordinates.Rd ├── rotate_igraph_layout.Rd ├── score_gene_path_clusters.Rd ├── shape.coloredrectangle.plot.Rd ├── shape.ellipse.clip.Rd ├── shape.ellipse.plot.Rd ├── shape.jampie.plot.Rd ├── shinycat_server.Rd ├── shinycat_ui.Rd ├── spread_igraph_labels.Rd ├── subgraph_jam.Rd ├── subsetCnetIgraph.Rd ├── subset_igraph_components.Rd ├── summarize_node_spacing.Rd ├── sync_igraph_communities.Rd ├── topEnrichBySource.Rd ├── with_ht_opts.Rd ├── with_qfr.Rd └── xyAngle.Rd ├── multienrichjam.Rproj ├── multienrichjam_dev_notes.md ├── multienrichjam_workflow_notes.md ├── tests ├── testthat.R └── testthat │ ├── _snaps │ └── mem-plots │ │ ├── gp-heatmap-column-cluster-function.svg │ │ 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