Function reference
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GO_similarity()guess_ont()random_GO() - Calculate Gene Ontology (GO) semantic similarity matrix
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anno_word_cloud() - Word cloud annotations
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anno_word_cloud_from_GO() - Word cloud annotations from GO
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area_above_ecdf() - Area above the eCDF curve
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plot_binary_cut()binary_cut() - Cluster functional terms by recursively binary cutting the similarity matrix
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register_clustering_methods()all_clustering_methods()remove_clustering_methods()reset_clustering_methods() - Configure clustering methods
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cluster_terms()cluster_by_kmeans()cluster_by_pam()cluster_by_dynamicTreeCut()cluster_by_fast_greedy()cluster_by_leading_eigen()cluster_by_louvain()cluster_by_walktrap()cluster_by_mclust()cluster_by_apcluster()cluster_by_hdbscan()cluster_by_MCL() - Cluster terms based on their similarity matrix
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cmp_make_clusters()cmp_make_plot()compare_clustering_methods() - Compare clustering methods
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count_words() - Calculate word frequency
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dend_node_apply()edit_node() - Apply functions on every node in a dendrogram
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difference_score() - Difference score
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export_to_shiny_app() - Interactively visualize the similarity heatmap
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ht_clusters() - Visualize the similarity matrix and the clustering
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keyword_enrichment_from_GO() - Keyword enrichment for GO terms
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partition_by_kmeans()partition_by_pam()partition_by_hclust()partition_by_kmeanspp() - Partition the matrix
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scale_fontsize() - Scale font size
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se_opt() - Global parameters
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select_cutoff() - Select the cutoff for binary cut
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simplifyGO()simplifyEnrichment() - Simplify Gene Ontology (GO) enrichment results
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simplifyGOFromMultipleLists() - Perform simplifyGO analysis with multiple lists of GO IDs
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summarizeGO() - A simplified way to visualize enrichment in GO clusters
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word_cloud_grob()widthDetails(<word_cloud>)heightDetails(<word_cloud>) - A simple grob for the word cloud