Package index

User-Facing Functions

Core functions

Functions central to multienrichjam

jam_igraph(): Jam custom function to plot an igraph network

mem_plot_folio() prepare_folio(): Multienrichment folio of summary plots

multiEnrichMap(): Prepare MultiEnrichMap data from enrichList

Import functions

Functions to use external data in multienrichjam

enrichDF2enrichResult(): Convert data.frame to enrichResult

importIPAenrichment(): Import Ingenuity Pathway Analysis 'IPA' results

IPAlist_to_hits(): Convert IPA list to a gene hit list or matrix

Other Useful Functions

Custom plot functions

Customized plotting for ‘Mem’ results

mem_enrichment_heatmap(): MultiEnrichment Heatmap of enrichment P-values

mem_gene_path_heatmap(): MultiEnrichment Heatmap of Genes and Pathways

mem_legend(): MultiEnrichMap color legend

igraph utilities

Utilities for igraph objects

color_edges_by_nodegroups(): Color edges by nodegroups

color_edges_by_nodes(): Colorize igraph edges by nodes

color_nodes_by_nodegroups(): Color edges by nodegroups

get_cnet_nodeset(): Get Cnet node set by connected Sets

jam_igraph(): Jam custom function to plot an igraph network

launch_shinycat(): Launch ShinyCAT: Cnet Adjustment Tool

subgraph_jam(): Subgraph using Jam extended logic

igraph layout functions

Layout functions for igraph objects

layout_with_qfr(): igraph layout using qgraph Fruchterman-Reingold

layout_with_qfrf(): igraph layout function using qgraph Fruchterman-Reingold

nudge_igraph_node(): Nudge igraph layout by node

relayout_with_qfr(): igraph re-layout using qgraph Fruchterman-Reingold

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

Cnet utilities

Utilities for Cnet igraph objects

adjust_cnet_nodeset(): Adjust Cnet node set

adjust_cnet_set_relayout_gene(): Adjust Set nodes then relayout Gene nodes

apply_nodeset_spacing(): Apply minimum node spacing for each Cnet node set

bulk_cnet_adjustments(): Bulk Cnet plot adjustments

get_cnet_nodeset(): Get Cnet node set by connected Sets

launch_shinycat(): Launch ShinyCAT: Cnet Adjustment Tool

make_cnet_test(): Make Cnet test igraph

Mem utilities

Functions useful for ‘Mem’ results

fixSetLabels() words abbrev: Fix Set or pathway labels for legibility

`[`(<Mem>,<ANY>,<ANY>,<ANY>) show(<Mem>) Mem_to_list() as.list(<Mem>) names(<Mem>) enrichments(<Mem>) `enrichments<-`(<Mem>) sets(<Mem>) `sets<-`(<Mem>) genes(<Mem>) `genes<-`(<Mem>) geneIM(<Mem>) geneIMdirection(<Mem>) `geneIMdirection<-`(<Mem>) geneIMcolors(<Mem>) `geneIMcolors<-`(<Mem>) enrichList(<Mem>) enrichIM(<Mem>) enrichIMcolors(<Mem>) `enrichIMcolors<-`(<Mem>) enrichIMdirection(<Mem>) `enrichIMdirection<-`(<Mem>) enrichIMgeneCount(<Mem>) memIM(<Mem>) geneHitIM(<Mem>) `geneHitIM<-`(<Mem>) geneHitList(<Mem>) `geneHitList<-`(<Mem>) headers(<Mem>) colorV(<Mem>) `colorV<-`(<Mem>) thresholds(<Mem>) `thresholds<-`(<Mem>) dim(<Mem>) dimnames(<Mem>) list_to_Mem() updateObject(<Mem>) geneInCategory(<Mem>) setsByGene(<Mem>): Mem S4 class, accessors, getters, and setters

mem2cnet() memIM2cnet(): Convert MultiEnrichment incidence matrix to Cnet plot

mem2emap(): Convert multiEnrichMap mem output to EnrichmentMap emap

list_to_MemPlotFolio() MemPlotFolio_to_list() show(<MemPlotFolio>) Clusters(<MemPlotFolio>) GeneClusters(<MemPlotFolio>) thresholds(<MemPlotFolio>) metadata(<MemPlotFolio>) Caption(<MemPlotFolio>) CaptionLegendList(<MemPlotFolio>) EnrichmentHeatmap(<MemPlotFolio>) GenePathHeatmap(<MemPlotFolio>) CnetCollapsed(<MemPlotFolio>) CnetExemplar(<MemPlotFolio>) CnetCluster(<MemPlotFolio>): Mem S4 class, accessors, getters, and setters

Functions Deep in the Details

Enrichment-supporting functions

Functions that manipulate enrichment or multiple enrichment results.

add_pathway_direction(): Add directionality to pathway enrichment

topEnrichBySource() topEnrichListBySource(): Subset enrichResult for top enrichment results by source

Plot support functions

Functions to plot MultiEnrichment results

adjust_polygon_border() adjust_rect_border(): Adjust polygon border to inner or outer edge

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

enrichList2df(): Convert enrichList to data.frame

enrichList2IM(): Convert enrichList to IM incidence matrix

Functions that extend or customize igraph-related features

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

fixSetLabels() words abbrev: Fix Set or pathway labels for legibility

flip_edges(): Flip direction of igraph edges

get_bipartite_nodeset(): Get partite/connected graph nodesets

highlight_edges_by_node(): Highlight edges connected to a node or nodes

igraph2pieGraph(): Convert igraph to use pie node shapes

label_communities(): Assign labels to igraph communities

mem2cnet() memIM2cnet(): Convert MultiEnrichment incidence matrix to Cnet plot

mem2emap(): Convert multiEnrichMap mem output to EnrichmentMap emap

nodegroups2communities(): Convert nodegroups list to communities object

rectifyPiegraph(): Convert pie igraph node shapes to coloredrectangle

removeIgraphBlanks(): Remove igraph blank wedges

subsetCnetIgraph(): Subset Cnet igraph

subset_igraph_components(): Subset igraph by connected components

sync_igraph_communities(): Sync igraph nodes and communities

Functions specific to Cnet igraph objects

apply_cnet_direction(): Apply Cnet border color by directionality

rotate_igraph_layout(): Rotate igraph layout coordinates

R-shiny functions

Functions supporting ShinyCat

launch_shinycat(): Launch ShinyCAT: Cnet Adjustment Tool

shinycat_server(): R-shiny server function for shinycat

shinycat_ui(): R-shiny ui function for shinycat

Mem functions

Functions supporting Mem S4 object use

check_Mem(): Check Mem object

`[`(<Mem>,<ANY>,<ANY>,<ANY>) show(<Mem>) Mem_to_list() as.list(<Mem>) names(<Mem>) enrichments(<Mem>) `enrichments<-`(<Mem>) sets(<Mem>) `sets<-`(<Mem>) genes(<Mem>) `genes<-`(<Mem>) geneIM(<Mem>) geneIMdirection(<Mem>) `geneIMdirection<-`(<Mem>) geneIMcolors(<Mem>) `geneIMcolors<-`(<Mem>) enrichList(<Mem>) enrichIM(<Mem>) enrichIMcolors(<Mem>) `enrichIMcolors<-`(<Mem>) enrichIMdirection(<Mem>) `enrichIMdirection<-`(<Mem>) enrichIMgeneCount(<Mem>) memIM(<Mem>) geneHitIM(<Mem>) `geneHitIM<-`(<Mem>) geneHitList(<Mem>) `geneHitList<-`(<Mem>) headers(<Mem>) colorV(<Mem>) `colorV<-`(<Mem>) thresholds(<Mem>) `thresholds<-`(<Mem>) dim(<Mem>) dimnames(<Mem>) list_to_Mem() updateObject(<Mem>) geneInCategory(<Mem>) setsByGene(<Mem>): Mem S4 class, accessors, getters, and setters

Memtest Reese_genes: Reese 2019 cohort multienrichment data

Mem-slots: Mem description of slots

MemPlotFolio functions

Functions supporting MemPlotFolio S4 object use

check_MemPlotFolio(): Check MemPlotFolio object

list_to_MemPlotFolio() MemPlotFolio_to_list() show(<MemPlotFolio>) Clusters(<MemPlotFolio>) GeneClusters(<MemPlotFolio>) thresholds(<MemPlotFolio>) metadata(<MemPlotFolio>) Caption(<MemPlotFolio>) CaptionLegendList(<MemPlotFolio>) EnrichmentHeatmap(<MemPlotFolio>) GenePathHeatmap(<MemPlotFolio>) CnetCollapsed(<MemPlotFolio>) CnetExemplar(<MemPlotFolio>) CnetCluster(<MemPlotFolio>): Mem S4 class, accessors, getters, and setters

score_gene_path_clusters(): Score Gene-Path Clusters in MemPlotFolio

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

imSigned2list(): convert signed incidence matrix to list

list2concordance(): Convert list to concordance matrix

list2im(): convert list to incidence matrix

list2imSigned(): convert list to directional incidence matrix

Utility functions

Functions used by other multienrichjam functions

ashape(): Alpha shape calculation

avg_angles(): Average geometric angles

avg_colors_by_list(): Average colors by list

cell_fun_bivariate(): ComplexHeatmap cell function with bivariant color

collapse_mem_clusters(): Collapse Multienrichment clusters

colorRamp2D(): Color ramp for bivariate colors

curateIPAcolnames(): Curate Ingenuity IPA colnames

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

find_colname(): Find colname by character string or pattern matching

find_enrich_colnames(): Find enrichment colnames

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 recommended overlap threshold for EnrichMap

order_colors(): Order colors

rank_mem_clusters(): Rank Multienrichment clusters

rotate_coordinates(): Rotate numeric coordinates

summarize_node_spacing(): Summarize spacing between igraph nodes or node groups

with_ht_opts() local_ht_opts(): Withr mimic of with_options() for ComplexHeatmap options

xyAngle(): Get angle from origin to vector of x,y coordinates

Import functions

Functions to import enrichment data

enrichDF2enrichResult(): Convert data.frame to enrichResult

importIPAenrichment(): Import Ingenuity Pathway Analysis 'IPA' results

IPAlist_to_hits(): Convert IPA list to a gene hit list or matrix

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

jam_plot_igraph(): Jam igraph vectorized plot function (internal)

Deprecated functions

Functions moved or removed

cnetplotJam(): Create a cnetplot igraph object, deprecated

enrichMapJam(): Create enrichMap igraph object from enrichResult, deprecated

grid_with_title(): Draw Heatmap with title and subtitle using grid viewports, deprecated

mem_multienrichplot(): MultiEnrichMap plot

with_qfr(): Layout specification for Qgraph Fruchterman-Reingold, deprecated

User-Facing Functions

Core functions

Import functions

Other Useful Functions

Custom plot functions

igraph utilities

igraph layout functions

Cnet utilities

Mem utilities

Functions Deep in the Details

Enrichment-supporting functions

Plot support functions

Conversion functions

Detailed igraph-related functions

Cnet igraph-related functions

R-shiny functions

Mem functions

MemPlotFolio functions

igraph vertex shapes

list functions

Utility functions

Import functions

Internal igraph functions

Deprecated functions