Files in jmw86069/multienrichjam

Analysis and Visualization of Multiple Gene Set Enrichments

.Rbuildignore

.gitignore

DESCRIPTION

MultiEnrichMap_notes.Rmd

NAMESPACE

NEWS.md R/jam-call-fn-ellipsis.R R/jam-deconcat.R R/jam-igraph-internals.R R/jam-igraph-plot.R R/jam-points-to-ahull.R R/jam-polygon-borders.R R/jamenrich-apply-cnet-direction.R R/jamenrich-base.r R/jamenrich-bivariatecolor.R R/jamenrich-cnet.R R/jamenrich-color-nodes-edges.R R/jamenrich-communities-nodegroups.R R/jamenrich-enrichdf2er.R R/jamenrich-get-igraph-layout.R R/jamenrich-igraph.r R/jamenrich-igraphshapes.R R/jamenrich-import.R R/jamenrich-jam-plot-igraph.R R/jamenrich-make-cnet-test.R R/jamenrich-mem2cnet.R R/jamenrich-mem2emap.R R/jamenrich-plot.R R/jamenrich-rotate.R R/jamenrich-sets.r R/jamenrich-subset-mem.R R/jamenrich-summarize-node-spacing.R R/jamenrich-topenrich.R R/jamenrich-utils.R R/jamgraph-edgebundle.R README.Rmd README.md TODO.md TODO_freshenGenes.md

_pkgdown.yml

cnet_heatmap_guide.md

docs/404.html

docs/TODO.html

docs/TODO_freshenGenes.html

docs/articles/importIPA.html

docs/articles/importIPA_files/accessible-code-block-0.0.1/empty-anchor.js

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docs/articles/index.html

docs/authors.html

docs/bootstrap-toc.css

docs/bootstrap-toc.js

docs/cnet_heatmap_guide.html

docs/docsearch.css

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docs/mem_function_notes.html

docs/news/index.html

docs/pkgdown.css

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docs/pkgdown.yml

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docs/reference/cnet2df.html

docs/reference/cnet2im.html

docs/reference/cnetplotJam.html

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docs/reference/communities2nodegroups.html

docs/reference/curateIPAcolnames.html

docs/reference/deconcat_df2.html

docs/reference/default_igraph_values.html

docs/reference/display_colorRamp2D.html

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docs/reference/enrichDF2enrichResult.html

docs/reference/enrichList2IM.html

docs/reference/enrichList2df.html

docs/reference/enrichList2geneHitList.html

docs/reference/enrichMapJam.html

docs/reference/filter_mem_genes.html

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docs/reference/get_bipartite_nodeset.html

docs/reference/get_cnet_nodeset.html

docs/reference/get_igraph_arrow_mode.html

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docs/reference/grid_with_title.html

docs/reference/gsubs.html

docs/reference/handle_igraph_param_list.html

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docs/reference/jam_mypie.html

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docs/reference/mem2emap.html

docs/reference/memIM2cnet.html

docs/reference/mem_enrichment_heatmap.html

docs/reference/mem_find_overlap.html

docs/reference/mem_gene_path_heatmap.html

docs/reference/mem_legend.html

docs/reference/mem_multienrichplot.html

docs/reference/mem_plot_folio.html

docs/reference/mergeAllXY.html

docs/reference/multiEnrichMap.html

docs/reference/nodegroups2communities.html

docs/reference/nudge_igraph_node.html

docs/reference/order_colors.html

docs/reference/parse_igraph_plot_params.html

docs/reference/plot_layout_scale.html

docs/reference/rank_mem_clusters.html

docs/reference/rectifyPiegraph.html

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docs/reference/spread_igraph_labels.html

docs/reference/subgraph_jam.html

docs/reference/subsetCnetIgraph.html

docs/reference/subset_igraph_components.html

docs/reference/subset_mem.html

docs/reference/summarize_node_spacing.html

docs/reference/sync_igraph_communities.html

docs/reference/topEnrichBySource.html

docs/reference/topEnrichListBySource.html

docs/reference/unnestList.html

docs/reference/with_qfr.html

docs/reference/xyAngle.html

docs/sitemap.xml

inst/extdata/Newborns-IPA.txt

inst/extdata/OlderChildren-IPA.txt

man/adjust_cnet_nodeset.Rd man/adjust_cnet_set_relayout_gene.Rd man/adjust_polygon_border.Rd man/apply_cnet_direction.Rd man/apply_nodeset_spacing.Rd man/avg_angles.Rd man/avg_colors_by_list.Rd man/call_fn_ellipsis_deprecated.Rd man/cell_fun_bivariate.Rd man/cnet2df.Rd man/cnet2im.Rd man/cnetplotJam.Rd man/cnetplot_internalJam.Rd man/collapse_mem_clusters.Rd man/colorRamp2D.Rd man/color_edges_by_nodegroups.Rd man/color_edges_by_nodes.Rd man/color_edges_by_nodes_deprecated.Rd man/color_nodes_by_nodegroups.Rd man/colors_from_list.Rd man/communities2nodegroups.Rd man/curateIPAcolnames.Rd man/deconcat_df2.Rd man/default_igraph_values.Rd man/display_colorRamp2D.Rd man/drawEllipse.Rd man/edge_bundle_bipartite.Rd man/edge_bundle_nodegroups.Rd man/enrichDF2enrichResult.Rd man/enrichList2IM.Rd man/enrichList2df.Rd man/enrichList2geneHitList.Rd man/enrichMapJam.Rd man/filter_mem_genes.Rd man/filter_mem_sets.Rd man/find_colname.Rd man/fixSetLabels.Rd man/flip_edges.Rd man/get_bipartite_nodeset.Rd man/get_cnet_nodeset.Rd man/get_igraph_arrow_mode.Rd man/get_igraph_layout.Rd man/grid_with_title.Rd man/gsubs.Rd man/handle_igraph_param_list.Rd man/heatmap_column_order_deprecated.Rd man/heatmap_row_order_deprecated.Rd man/igraph2pieGraph.Rd man/im2list.Rd man/im2list_dep.Rd man/imSigned2list.Rd man/imSigned2list_dep.Rd man/importIPAenrichment.Rd man/isColorBlank.Rd man/jam_igraph.Rd man/jam_igraph_arrows.Rd man/jam_mypie.Rd man/jam_plot_igraph.Rd man/label_communities.Rd man/layout_with_qfr.Rd man/layout_with_qfrf.Rd man/list2concordance.Rd man/list2im.Rd man/list2imSigned.Rd man/make_cnet_test.Rd man/make_legend_bivariate.Rd man/make_point_hull.Rd man/mem2emap.Rd man/memIM2cnet.Rd man/mem_enrichment_heatmap.Rd man/mem_find_overlap.Rd man/mem_gene_path_heatmap.Rd man/mem_legend.Rd man/mem_multienrichplot.Rd man/mem_plot_folio.Rd man/multiEnrichMap.Rd man/nodegroups2communities.Rd man/nudge_igraph_node.Rd man/order_colors.Rd man/parse_igraph_plot_params.Rd man/plot_layout_scale.Rd man/rank_mem_clusters.Rd man/rectifyPiegraph.Rd man/relayout_with_qfr.Rd man/removeIgraphBlanks.Rd man/removeIgraphSinglets.Rd man/reorderIgraphNodes.Rd man/rotate_coordinates.Rd man/rotate_igraph_layout.Rd man/shape.coloredrectangle.plot.Rd man/shape.ellipse.clip.Rd man/shape.ellipse.plot.Rd man/shape.jampie.plot.Rd man/sort_colors_deprecated.Rd man/spread_igraph_labels.Rd man/subgraph_jam.Rd man/subsetCnetIgraph.Rd man/subset_igraph_components.Rd man/subset_mem.Rd man/summarize_node_spacing.Rd man/sync_igraph_communities.Rd man/topEnrichBySource.Rd man/with_qfr.Rd man/xyAngle.Rd mem_function_notes.md

multienrichjam.Rproj

vignettes/.gitignore

vignettes/importIPA.Rmd

jmw86069/multienrichjam documentation built on Feb. 7, 2024, 12:58 a.m.