Function reference • GeneTonic

All functions
`GeneTonic()`	GeneTonic
`GeneTonicList()` `GeneTonic_list()`	Create a GeneTonicList object
`check_colors()`	Check colors
`checkup_GeneTonic()`	Checking the input objects for GeneTonic
`checkup_gtl()`	Checking the `gtl` input object for GeneTonic
`cluster_markov()`	Markov Clustering (MCL) for community detection
`create_jaccard_matrix()`	Compute the overlap matrix for enrichment results
`create_kappa_matrix()`	Compute the kappa matrix for enrichment results
`create_upsetdata()`	Create a geneset upset dataset
`describe_gtl()`	Describe a GeneTonic list
`deseqresult2df()`	Generate a table from the `DESeq2` results
`distill_enrichment()`	Distill enrichment results
`.check_pandoc()`	Check whether `pandoc` and `pandoc-citeproc` are available
`editor_to_vector_sanitized()`	Extract vectors from editor content
`enhance_table()`	Visually enhances a functional enrichment result table
`enrichment_map()`	Creates an enrichment map for the results of functional enrichment
`enrichr_output_macrophage`	A sample output from Enrichr
`export_for_iSEE()`	export_for_iSEE
`export_to_sif()`	Export to sif
`fgseaRes`	A sample output from fgsea
`gene_plot()`	Plot expression values for a gene
`geneinfo_2_html()`	Information on a gene
`get_aggrscores()`	Compute aggregated scores for gene sets
`get_expression_values()`	Get expression values
`ggs_backbone()`	Extract the backbone for the gene-geneset graph
`ggs_graph()`	Construct a gene-geneset-graph
`go_2_html()`	Information on a GeneOntology identifier
`gostres_macrophage`	A sample output from g:Profiler
`gs_alluvial()` `gs_sankey()`	Alluvial (sankey) plot for a set of genesets and the associated genes
`gs_dendro()`	Dendrogram of the gene set enrichment results
`gs_fuzzyclustering()`	Compute fuzzy clusters of gene sets
`gs_heatmap()`	Plot a heatmap of the gene signature on the data
`gs_horizon()`	Plots a summary of enrichment results
`gs_mds()`	Multi Dimensional Scaling plot for gene sets
`gs_radar()` `gs_spider()`	Radar (spider) plot for gene sets
`gs_scores()`	Compute gene set scores
`gs_scoresheat()`	Plots a matrix of geneset scores
`gs_simplify()`	Simplify results from functional enrichment analysis
`gs_summary_heat()`	Plots a heatmap for genes and genesets
`gs_summary_overview()`	Plots a summary of enrichment results
`gs_summary_overview_pair()`	Plots a summary of enrichment results
`gs_upset()`	Upset plot for genesets
`gs_volcano()`	Volcano plot for gene sets
`happy_hour()`	Happy hour!
`map2color()`	Maps numeric values to color values
`overlap_coefficient()`	Calculate overlap coefficient
`overlap_jaccard_index()`	Calculate Jaccard Index between two sets
`res_macrophage_IFNg_vs_naive`	A sample `DESeqResults` object
`shake_davidResult()`	Convert the output of DAVID
`shake_enrichResult()`	Convert an enrichResult object
`shake_enrichrResult()`	Convert the output of Enrichr
`shake_fgseaResult()`	Convert the output of fgsea
`shake_gprofilerResult()`	Convert the output of g:Profiler
`shake_gsenrichResult()`	Convert a gseaResult object
`shake_topGOtableResult()`	Convert a topGOtableResult object
`signature_volcano()`	Plot a volcano plot of a geneset
`styleColorBar_divergent()`	Style DT color bars
`summarize_ggs_hubgenes()`	Summarize information on the hub genes
`topgoDE_macrophage_IFNg_vs_naive`	A sample `res_enrich` object

Reference

All functions