_pkgdown.yml

url: https://david-barnett.github.io/microViz/
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toc:
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navbar:
  structure:
    left:
    - start
    - reference
    - articles
    - learn
    - news
    - intro
    right: github
  components:
    home: ~
    start:
      text: Getting Started
      href: articles/shao19-analyses.html
    reference:
      text: Reference
      href: reference/index.html
    articles:
      text: Articles
      menu:
      - text: Working with phyloseq objects
        href: articles/web-only/phyloseq.html
      - text: Fixing your tax_table
        href: articles/web-only/tax-fixing.html
      - text: Ordination plots
        href: articles/web-only/ordination.html
      - text: Interactive ordination plots
        href: articles/web-only/ordination-interactive.html
      - text: Visualising compositions with barplots
        href: articles/web-only/compositions.html
      - text: Heatmaps of microbiome composition or correlation
        href: articles/web-only/heatmaps.html
      - text: Statistical modelling of individual taxa
        href: articles/web-only/modelling-taxa.html
      - text: Tutorial video
        href: articles/web-only/videos.html
      - text: "Upgrading to microViz version 0.10.0"
        href: articles/ps_extra-replaced.html
      - text: Example analyses with atlas1006 data
        href: articles/web-only/atlas1006.html
    learn:
      text: Learn
      href: articles/learn/exercises.html
    news:
      text: News
      href: news/index.html
    intro:
      text: ''
redirects:
  - ["articles/microViz.html", "index.html"]
reference:
- title: Subsetting or sorting phyloseq samples
  desc: |
    Functions for filtering or reording samples in a phyloseq object.
    These characteristically start with "ps_", which is short for phyloseq.
- contents:
  - ps_filter
  - ps_arrange
  - ps_seriate
  - ps_sort_ord
  - ps_reorder
  - ps_dedupe
  - ps_drop_incomplete
- title: Manipulating phyloseq sample_data
  desc: |
    Functions for modifying and augmenting the sample data within phyloseq objects.
    These also start with "ps_", which is short for phyloseq.
- contents:
  - ps_select
  - ps_mutate
  - ps_join
  - ps_otu2samdat
  - ps_melt
- title: Manipulating taxa
  desc: |
    Functions for modifying the taxonomic information contained within phyloseq objects.
    These characteristically start with "tax_", which is short for taxa.
- contents:
  - tax_fix
  - tax_fix_interactive
  - tax_prepend_ranks
  - tax_filter
  - tax_agg
  - tax_transform
  - tax_scale
  - tax_select
  - tax_mutate
  - tax_rename
  - tax_name
  - tax_sort
  - tax_sort_ord
  - tax_reorder
  - tax_top
  - tax_names2rank
- title: Ordination and related methods
  desc: |
    Functions for assessing and visualising overall microbiota composition and its associations with phyloseq sample data variables.
    dist_* functions calculate or use sample-sample distances/dissimilarities.
    ord_* functions calculate or use sample ordinations.
- contents:
  - dist_calc
  - dist_permanova
  - dist_bdisp
  - ord_calc
  - ord_plot
  - stat_chull
  - add_paths
  - Ordination-labels
  - Ordination-arrows
  - ord_plot_iris
  - ord_explore
  - scale_shape_girafe_filled
  - psExtra-accessors
- title: Taxon models and tree visualisations
  desc: |
    Functions for modelling and visualising associations between individual microbes and phyloseq sample data variables.
- contents:
  - tax_model
  - taxatree_models
  - taxatree_models2stats
  - taxatree_stats_p_adjust
  - taxatree_plots
  - taxatree_plotkey
  - taxatree_label
  - taxatree_plot_labels
  - taxatree_funs
  - cor_test
- title: Heatmap plotting functions
  desc: |
    Functions for drawing and annotating heatmaps
- contents:
  - comp_heatmap
  - cor_heatmap
  - taxAnnotation
  - anno_tax_box
  - anno_tax_prev
  - anno_tax_density
  - sampleAnnotation
  - anno_sample
  - anno_sample_cat
  - anno_cat
  - anno_cat_legend
  - varAnnotation
  - anno_var_box
  - anno_var_hist
  - anno_var_density
  - heat_palette
  - heat_numbers
  - heat_grid
  - adjacent_side
- title: Other functions
  desc: |
    Other assorted functions
- contents:
  - comp_barplot
  - distinct_palette
  - tax_palette
  - tax_palette_plot
  - ps_calc_dominant
  - ps_calc_diversity
  - ps_calc_richness
  - phyloseq_validate
  - prev
- title: Datasets
- contents:
  - shao19
  - ibd
- title: Other
- contents:
  - microViz
  - print.psExtraInfo
  - psExtra-class
  - upgrade_ps_extra_to_psExtra
  - dist_calc_seq
  - deprecated-heatmap-annotations