_pkgdown.yml

url: https://jeffkimbrel.github.io/jakR/
template:
  bootstrap: 5
  bslib:
    bg: "#202123"
    fg: "#B8BCC2"
    primary: "#037bcf"

reference:
- title: Color Palettes
  contents:
  - palette_jak
  - show_color_palette
  - show_all_color_palettes
  - expand_named_palette
  - get_phylo_palette
  - jak_palettes

- title: Microbial Communities
  contents:
  - get_alpha_diversity
  - get_phylo_diversity
  - permanova
  - pairwiseAdonis
  - phylo_other
  - plot_distances
  - plotPD
  - zeroOTU

- title: Genomics
  contents:
  - fastq_filter_summary_amplicon
  - fastq_filter_summary_meta
  - fastq_info_summary
  - run_fts
  - get_fts_intervals
  - plot_fts_intervals
  - plot_fts_points
  - getSig
  - sigCombine
  - orthofinder_complete_clusters
  - orthofinder_summary
  - drep_extract
  - seqtab_stats
  - illumina_codes

- title: Misc
  contents:
  - jak_theme
  - format_dt
  - gt_theme

- title: internal
  contents:
  - all_are_valid_colors
  - getAlphaDiversity
  - getPhyloDiversity
  - jak_theme_black
  - summarySE
  - plotDistances