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  "Title": "Microbiome Data Analysis and Visualization",
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  "Date/Publication": "2026-06-01 18:04:22 UTC",
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    "sampleAnnotation",
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    "stat_chull",
    "tax_agg",
    "tax_anno",
    "tax_filter",
    "tax_fix",
    "tax_fix_interactive",
    "tax_lab_style",
    "tax_model",
    "tax_models_get",
    "tax_models2stats",
    "tax_mutate",
    "tax_name",
    "tax_names2rank",
    "tax_palette",
    "tax_palette_plot",
    "tax_prepend_ranks",
    "tax_rename",
    "tax_reorder",
    "tax_scale",
    "tax_select",
    "tax_sort",
    "tax_sort_ord",
    "tax_stats_get",
    "tax_top",
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    "taxAnnotation",
    "taxatree_edges",
    "taxatree_label",
    "taxatree_models",
    "taxatree_models_get",
    "taxatree_models2stats",
    "taxatree_nodes",
    "taxatree_plot_labels",
    "taxatree_plotkey",
    "taxatree_plots",
    "taxatree_stats_get",
    "taxatree_stats_p_adjust",
    "textAngleCalc",
    "textHjustCalc",
    "tt_get",
    "upgrade_ps_extra_to_psExtra",
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    "vec_tax_all",
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  "_datasets": [
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      "name": "ibd",
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      "object": "ibd",
      "class": [
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      "fields": [],
      "table": false,
      "tojson": false
    },
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      "object": "shao19",
      "class": [
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      "fields": [],
      "table": false,
      "tojson": false
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      "topics": [
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    {
      "page": "adjacent_side",
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      "page": "anno_cat",
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      "topics": [
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      "page": "anno_cat_legend",
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    },
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      "topics": [
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    {
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      "topics": [
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    {
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    {
      "page": "comp_barplot",
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    },
    {
      "page": "comp_heatmap",
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    {
      "page": "cor_heatmap",
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    {
      "page": "cor_test",
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      "topics": [
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    },
    {
      "page": "deprecated-heatmap-annotations",
      "title": "DEPRECATED Heatmap annotations helpers",
      "topics": [
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        "anno_prev",
        "deprecated-heatmap-annotations",
        "old_anno_var_box",
        "old_anno_var_hist",
        "tax_anno",
        "var_anno"
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    },
    {
      "page": "dist_bdisp",
      "title": "Wrapper for vegan::betadisper()",
      "topics": [
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    },
    {
      "page": "dist_calc",
      "title": "Calculate distances between pairs of samples in phyloseq object",
      "topics": [
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    },
    {
      "page": "dist_calc_seq",
      "title": "Calculate distances between sequential samples in ps_extra/phyloseq object",
      "topics": [
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    },
    {
      "page": "dist_permanova",
      "title": "Calculate PERMANOVA after dist_calc()",
      "topics": [
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    },
    {
      "page": "distinct_palette",
      "title": "Colour palettes suitable for 20+ categories",
      "topics": [
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    },
    {
      "page": "heat_grid",
      "title": "set options for drawing gridlines on heatmaps",
      "topics": [
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    },
    {
      "page": "heat_numbers",
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    },
    {
      "page": "heat_palette",
      "title": "Easy palettes for ComplexHeatmap",
      "topics": [
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    },
    {
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      "title": "IBD study data in phyloseq object.",
      "topics": [
        "ibd"
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    },
    {
      "page": "microViz",
      "title": "microViz: microbiome data analysis and visualization",
      "topics": [
        "microViz-package",
        "microViz"
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    },
    {
      "page": "ord_calc",
      "title": "Ordinate samples (arrange by similarity in multiple dimensions)",
      "topics": [
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    },
    {
      "page": "ord_explore",
      "title": "Interactively explore microbial compositions of ordinated samples",
      "topics": [
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      ]
    },
    {
      "page": "ord_plot",
      "title": "Customisable ggplot2 ordination plot",
      "topics": [
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    },
    {
      "page": "ord_plot_iris",
      "title": "Circular compositional barplot sorted by ordination angle",
      "topics": [
        "ord_plot_iris"
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    },
    {
      "page": "ord_arrows",
      "title": "Create ordination plot vector styling lists",
      "topics": [
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        "vec_constraint",
        "vec_tax_all",
        "vec_tax_sel"
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    },
    {
      "page": "Ordination-labels",
      "title": "Create list for ord_plot() *_lab_style arguments",
      "topics": [
        "constraint_lab_style",
        "Ordination-labels",
        "tax_lab_style"
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      "topics": [
        "phyloseq_validate"
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    },
    {
      "page": "prev",
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      "topics": [
        "prev"
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    },
    {
      "page": "psExtraInfo",
      "title": "Print method for psExtraInfo object",
      "topics": [
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    {
      "page": "ps_arrange",
      "title": "Arrange samples in phyloseq by sample_data variables or taxon abundance",
      "topics": [
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    },
    {
      "page": "ps_calc_diversity",
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    },
    {
      "page": "ps_calc_dominant",
      "title": "Calculate dominant taxon in each phyloseq sample",
      "topics": [
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    },
    {
      "page": "ps_calc_richness",
      "title": "Calculate richness estimate and add to phyloseq sample data",
      "topics": [
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    {
      "page": "ps_dedupe",
      "title": "De-duplicate phyloseq samples",
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    },
    {
      "page": "ps_drop_incomplete",
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      "topics": [
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    },
    {
      "page": "ps_filter",
      "title": "Filter phyloseq samples by sample_data variables",
      "topics": [
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      ]
    },
    {
      "page": "ps_join",
      "title": "Join a dataframe to phyloseq sample data",
      "topics": [
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    },
    {
      "page": "ps_melt",
      "title": "Melt phyloseq data object into large data.frame (tibble)",
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    },
    {
      "page": "ps_mutate",
      "title": "Modify or compute new sample_data in phyloseq object",
      "topics": [
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