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  "Title": "Visualising Sets of Ontological Terms",
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  "Author": "Daniel Greene <dg333@cam.ac.uk>",
  "Maintainer": "Daniel Greene <dg333@cam.ac.uk>",
  "Description": "Create R plots visualising ontological terms and the\nrelationships between them with various graphical options -\nGreene et al. 2017 <doi:10.1093/bioinformatics/btw763>.",
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    "calibrate_sizes",
    "colour_by_frequency",
    "colour_by_population_frequency",
    "colour_by_term_set",
    "dot_string",
    "get_adjacency_matrix",
    "get_node_friendly_long_names",
    "get_pseudo_adjacency_matrix",
    "get_shortened_names",
    "grid_terms",
    "label_by_frequency",
    "label_by_term_set",
    "long_labels",
    "n_most_frequent_terms",
    "official_labels",
    "onto_plot",
    "p_values_for_occurrence_of_term_in_group",
    "plot_annotation_grid",
    "remove_links",
    "remove_terms_with_less_than_n_occurrences",
    "remove_uninformative_terms",
    "simple_cap",
    "simple_labels",
    "width_by_frequency",
    "width_by_significance",
    "write_dot"
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    {
      "page": "annotation_grid",
      "title": "Get logical matrix of term annotation for group of cases",
      "topics": [
        "annotation_grid"
      ]
    },
    {
      "page": "calibrate_sizes",
      "title": "Function to scale values between two given limits",
      "topics": [
        "calibrate_sizes"
      ]
    },
    {
      "page": "colour_by_frequency",
      "title": "Function to assign colours to terms based on frequency with which terms appear in 'term_sets'",
      "topics": [
        "colour_by_frequency"
      ]
    },
    {
      "page": "colour_by_population_frequency",
      "title": "Function to assign colours to terms based on population frequency of terms",
      "topics": [
        "colour_by_population_frequency"
      ]
    },
    {
      "page": "colour_by_term_set",
      "title": "Function to set colours of nodes in plot to distinguish terms belonging to different term sets",
      "topics": [
        "colour_by_term_set"
      ]
    },
    {
      "page": "dot_string",
      "title": "'ontology_plot' object to dot string",
      "topics": [
        "dot_string"
      ]
    },
    {
      "page": "get_adjacency_matrix",
      "title": "Get an adjacency matrix for a set of ontological terms",
      "topics": [
        "get_adjacency_matrix"
      ]
    },
    {
      "page": "get_node_friendly_long_names",
      "title": "Split up node labels across lines so they fit in nodes better",
      "topics": [
        "get_node_friendly_long_names"
      ]
    },
    {
      "page": "get_ontology_plot",
      "title": "Get 'ontology_plot' object",
      "topics": [
        "get_ontology_plot"
      ]
    },
    {
      "page": "get_pseudo_adjacency_matrix",
      "title": "Get an adjacency matrix for a set of ontological terms",
      "topics": [
        "get_pseudo_adjacency_matrix"
      ]
    },
    {
      "page": "get_shortened_names",
      "title": "Get human readable, shortened (where possible) ontological term names",
      "topics": [
        "get_shortened_names"
      ]
    },
    {
      "page": "grid_terms",
      "title": "Get set of HPO terms appropriate for showing in a grid",
      "topics": [
        "grid_terms"
      ]
    },
    {
      "page": "label_by_frequency",
      "title": "Function to get plot labels for terms based on frequency in 'term_sets'",
      "topics": [
        "label_by_frequency"
      ]
    },
    {
      "page": "label_by_term_set",
      "title": "Function to label nodes by 'term_set'",
      "topics": [
        "label_by_term_set"
      ]
    },
    {
      "page": "long_labels",
      "title": "Function to assign detailed node labels to terms",
      "topics": [
        "long_labels"
      ]
    },
    {
      "page": "n_most_frequent_terms",
      "title": "Select 'n' most prevalent terms in 'term_sets'",
      "topics": [
        "n_most_frequent_terms"
      ]
    },
    {
      "page": "official_labels",
      "title": "Get official names for terms",
      "topics": [
        "official_labels"
      ]
    },
    {
      "page": "onto_plot",
      "title": "Get 'ontology_plot' object",
      "topics": [
        "onto_plot"
      ]
    },
    {
      "page": "ontologyPlot-package",
      "title": "Functions for Visualising Sets of Ontological Terms",
      "topics": [
        "ontologyPlot-package",
        "ontologyPlot"
      ]
    },
    {
      "page": "p_values_for_occurrence_of_term_in_group",
      "title": "Get p-values for observing at least as many of each term as occur in 'term_sets' given the population frequencies of the terms",
      "topics": [
        "p_values_for_occurrence_of_term_in_group"
      ]
    },
    {
      "page": "plot_annotation_grid",
      "title": "Plot a logical matrix of term annotation",
      "topics": [
        "plot_annotation_grid"
      ]
    },
    {
      "page": "plot.ontology_plot",
      "title": "Plotting function for 'ontology_plot' object",
      "topics": [
        "plot.ontology_plot"
      ]
    },
    {
      "page": "print.ontology_plot",
      "title": "Print function for 'ontology_plot' object",
      "topics": [
        "print.ontology_plot"
      ]
    },
    {
      "page": "remove_links",
      "title": "Remove terms which just link two other terms together in a subontology",
      "topics": [
        "remove_links"
      ]
    },
    {
      "page": "remove_terms_with_less_than_n_occurrences",
      "title": "Remove terms with less than certain number of occurrences",
      "topics": [
        "remove_terms_with_less_than_n_occurrences"
      ]
    },
    {
      "page": "remove_uninformative_terms",
      "title": "Remove uninformative terms from union of all terms in set of annotations",
      "topics": [
        "remove_uninformative_terms"
      ]
    },
    {
      "page": "simple_cap",
      "title": "Capitalise words in character vector",
      "topics": [
        "simple_cap"
      ]
    },
    {
      "page": "simple_labels",
      "title": "Get simplified labels for terms",
      "topics": [
        "simple_labels"
      ]
    },
    {
      "page": "to_svg_string",
      "title": "Convert 'ontology_plot' to SVG string",
      "topics": [
        "to_svg_string"
      ]
    },
    {
      "page": "width_by_frequency",
      "title": "Function to get node sizes for terms based on frequency in 'term_sets'",
      "topics": [
        "width_by_frequency"
      ]
    },
    {
      "page": "width_by_significance",
      "title": "Function to get node sizes for terms based on statistical significance of seeing at least this number of each term in 'term_sets'",
      "topics": [
        "width_by_significance"
      ]
    },
    {
      "page": "write_dot",
      "title": "Export 'ontology_plot' object as dot file",
      "topics": [
        "write_dot"
      ]
    }
  ],
  "_rundeps": [
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    "generics",
    "graph",
    "ontologyIndex",
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      "engine": "knitr::rmarkdown",
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