Function reference • multienrichjam

Enrichment functions Functions that manipulate enrichment or multiple enrichment results.
`add_pathway_direction()`	Add directionality to pathway enrichment
`multiEnrichMap()`	Prepare MultiEnrichMap data from enrichList
`topEnrichBySource()` `topEnrichListBySource()`	Subset enrichResult for top enrichment results by source
Plot functions Functions to plot MultiEnrichment results
`adjust_polygon_border()`	Adjust polygon border to inner or outer edge
`grid_with_title()`	Draw Heatmap with title and subtitle using grid viewports
`jam_igraph()`	Jam wrapper to plot igraph
`mem_enrichment_heatmap()`	MultiEnrichment Heatmap of enrichment P-values
`mem_gene_path_heatmap()`	MultiEnrichment Heatmap of Genes and Pathways
`mem_legend()`	MultiEnrichMap color legend
`mem_multienrichplot()`	MultiEnrichMap plot
`mem_plot_folio()`	Multienrichment folio of summary plots
`plot_layout_scale()`	Plot layout scale by percentage of coordinate range
Conversion functions Functions to convert data types
`cnet2df()`	Summarize Cnet igraph as a data.frame
`cnet2im()`	Convert Cnet igraph to incidence matrix
`enrichDF2enrichResult()`	Convert data.frame to enrichResult
`enrichList2IM()`	Convert enrichList to IM incidence matrix
`enrichList2df()`	Convert enrichList to data.frame
`enrichMapJam()`	Create enrichMap igraph object
igraph-related functions Functions that extend or customize igraph-related features
`cnet2df()`	Summarize Cnet igraph as a data.frame
`cnet2im()`	Convert Cnet igraph to incidence matrix
`cnetplotJam()`	Create a cnetplot igraph object
`cnetplot_internalJam()`	cnetplot internal function
`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
`communities2nodegroups()`	Convert communities object to nodegroups list format
`drawEllipse()`	Draw ellipse
`edge_bundle_bipartite()`	Bundle edges in a bipartite graph
`edge_bundle_nodegroups()`	Bundle edges using node groups
`enrichMapJam()`	Create enrichMap igraph object
`fixSetLabels()`	Fix Set labels for legibility
`flip_edges()`	Flip direction of igraph edges
`get_bipartite_nodeset()`	Get partite/connected graph nodesets
`igraph2pieGraph()`	Convert igraph to use pie node shapes
`jam_igraph()`	Jam wrapper to plot igraph
`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
`mem2emap()`	Convert multiEnrichMap mem output to EnrichmentMap emap
`memIM2cnet()` `mem2cnet()`	Convert MultiEnrichment incidence matrix to Cnet plot
`mem_multienrichplot()`	MultiEnrichMap plot
`nodegroups2communities()`	Convert nodegroups list to communities object
`nudge_igraph_node()`	Nudge igraph layout by node
`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()` `reorder_igraph_nodes()`	Re-order igraph nodes
`rotate_igraph_layout()`	Rotate igraph layout coordinates
`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
`sync_igraph_communities()`	Sync igraph nodes and communities
`with_qfr()`	Layout specification for Qgraph Fruchterman-Reingold
Cnet igraph-related functions Functions specific to Cnet igraph objects
`adjust_cnet_nodeset()`	Adjust Cnet node set
`adjust_cnet_set_relayout_gene()`	Adjust Set nodes then relayout Gene nodes
`apply_cnet_direction()`	Apply Cnet border color by directionality
`apply_nodeset_spacing()`	Apply minimum node spacing for each Cnet node set
`get_cnet_nodeset()`	Get Cnet node set by connected Sets
`make_cnet_test()`	Make Cnet test igraph
`nudge_igraph_node()`	Nudge igraph layout by node
`rotate_igraph_layout()`	Rotate igraph layout coordinates
igraph vertex shapes Functions that provide custom igraph vertex shapes
`jam_mypie()`	Vectorized mypie() function for igraph vertex pie polygons
`shape.coloredrectangle.plot()` `shape.coloredrectangle.clip()`	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()` `shape.jampie.clip()`	custom igraph vertex shape jampie
list functions Functions that operate on list objects
`colors_from_list()`	Ordered colors from a list of color vectors
`im2list()`	convert incidence matrix to list
`im2list_dep()`	convert incidence matrix to list
`imSigned2list()`	convert signed incidence matrix to list
`imSigned2list_dep()`	convert signed incidence matrix to list
`list2concordance()`	Convert list to concordance matrix
`list2im()`	convert list to incidence matrix
`list2imSigned()`	convert list to signeddirectional incidence matrix
Utility functions Functions used by other multienrichjam functions
`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
`collapse_mem_clusters()`	Collapse Multienrichment clusters
`colorRamp2D()`	Color ramp for bivariate colors
`deconcat_df2()`	Deconcatenate delimited column values in a data.frame
`display_colorRamp2D()`	Display colors from bivariate color function
`enrichList2geneHitList()`	Extract gene hit list from list of enrichResult
`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
`get_hull_data()`	Get data for alpha hull (internal)
`get_igraph_layout()`	Obtain or create layout for igraph object
`gsubs_remove()`	Pattern replacement with multiple patterns
`handle_igraph_param_list()`	Handle igraph attribute parameter list
`isColorBlank()`	Determine if colors are blank colors
`make_legend_bivariate()`	Display colors from bivariate color function
`make_point_hull()`	Make alpha hull from points
`mem_find_overlap()`	Find best overlap threshold for EnrichMap
`order_colors()`	Order colors
`rank_mem_clusters()`	Rank Multienrichment clusters
`rotate_coordinates()`	Rotate numeric coordinates
`subgraph_jam()`	Subgraph using Jam extended logic
`subset_mem()`	Subset mem multienrichment object
`summarize_node_spacing()`	Summarize spacing between igraph nodes given a layout
`xyAngle()`	Get angle from origin to vector of x,y coordinates
Import functions Functions to import enrichment data
`curateIPAcolnames()`	Curate Ingenuity IPA colnames
`importIPAenrichment()`	Import Ingenuity IPA enrichment results
Internal igraph functions Functions typically for internal use by other Jam functions, or which were internal igraph functions.
`default_igraph_values()`	Default igraph parameter values
`get_igraph_arrow_mode()`	Get igraph arrow mode
`jam_igraph_arrows()`	Render igraph arrows
`parse_igraph_plot_params()`	Parse igraph plot params
Deprecated functions Functions moved to the jamba package
`heatmap_column_order_deprecated()`	Return Heatmap column order
`heatmap_row_order_deprecated()`	Return Heatmap row order (deprecated)
`sort_colors_deprecated()`	Sort colors (deprecated)

Reference

Enrichment functions

Plot functions

Conversion functions

igraph-related functions

Cnet igraph-related functions

igraph vertex shapes

list functions

Utility functions

Import functions

Internal igraph functions

Deprecated functions