_pkgdown.yml

url: https://adrientaudiere.github.io/MiscMetabar/
template:
  bootstrap: 5
  bslib:
    bg: "#faefd1"
    fg: "#003f5f"
    primary: "#b96821"
    secondary: "#c8a734"
navbar:
  bg: secondary
  components:
   articles:
    text: Articles
    menu:
    - text: Tutorials
    - text: Import/export and track
      href: articles/import_export_track.html
    - text: Explore phyloseq data
      href: articles/explore_data.html
    - text: Filter taxa and samples
      href: articles/filter.html
    - text: Reclustering
      href: articles/Reclustering.html
    - text: Tree building and visualization
      href: articles/tree_visualization.html
    - text: -------
    - text: Diversity analysis
    - text: Alpha-diversity
      href: articles/alpha-div.html
    - text: Beta-diversity
      href: articles/beta-div.html
    - text: -------
    - text: Bioinformatics actions
    - text: Fastq quality check
      href: articles/fastq_quality_check.html
    - text: -------
    - text: Examples with published dataset
    - text: Tengeler dataset
      href: articles/tengeler.html
    - text: -------
    - text: "R ecosystem for metabarcoding"
    - text: "Metabarcoding with R"
      href: articles/states_of_fields_in_R.html
    - text: -------
    - text: "For developpers"
    - text: Rules of code
      href: articles/Rules.html
    - text: Report pkgnet
      href: articles/pkgnet-report.html

reference:
- title: Describe phyloseq object
- subtitle: See also vignette on [exploring data](articles/explore_data.html)
  contents:
  - summary_plot_pq
  - tbl_sum_samdata
  - tbl_sum_taxtable

- title: Transform phyloseq object
- subtitle: Verify and clean phyloseq object
  contents:
  - clean_pq
  - verify_pq

- subtitle: Taxonomy
  contents:
  - add_new_taxonomy_pq
  - add_blast_info
  - blast_to_phyloseq
  - blast_pq
  - blast_to_derep
  - filter_asv_blast
  - resolve_vector_ranks
  - assign_vsearch_lca
  - assign_sintax
  - assign_idtaxa
  - assign_blastn
  - learn_idtaxa

- subtitle: Function to add information from taxonomy
  contents:
  - add_funguild_info
  - funguild_assign
  - get_funguild_db

- subtitle: Transform OTU table only
  contents:
  - as_binary_otu_table
  - normalize_prop_pq
  - taxa_as_rows
  - taxa_as_columns

- subtitle: Subset/merge taxa
  contents:
  - subset_taxa_pq
  - subset_taxa_tax_control
  - select_taxa
  - merge_taxa_vec
  - filt_taxa_pq

- subtitle: Subset/merge samples
  contents:
  - merge_samples2
  - rarefy_sample_count_by_modality
  - select_one_sample
  - subset_samples_pq

- subtitle: (Re)clustering OTU table
  contents:
  - asv2otu
  - swarm_clustering
  - vsearch_clustering
  - lulu_pq
  - lulu
  - mumu_pq

- subtitle: Remove chimera using vsearch
  contents:
  - chimera_removal_vs
  - chimera_detection_vs

- subtitle: Sample data
  contents:
  - add_info_to_sam_data
  - sam_data_matching_names

- subtitle: Phylogenetic tree
  contents:
  - build_phytree_pq

- subtitle: References sequences
  contents:
  - add_dna_to_phyloseq
  - plot_complexity_pq
  - plot_refseq_extremity_pq
  - plot_refseq_pq

- title: Explore phyloseq object
- subtitle: alpha-diversity
  contents:
  - accu_plot
  - accu_plot_balanced_modality
  - accu_samp_threshold
  - ggbetween_pq
  - ggscatt_pq
  - glmutli_pq
  - hill_curves_pq
  - hill_pq
  - hill_test_rarperm_pq
  - hill_tuckey_pq
  - iNEXT_pq

- subtitle: beta-diversity
  contents:
  - adonis_pq
  - adonis_rarperm_pq
  - biplot_pq
  - circle_pq
  - compare_pairs_pq
  - formattable_pq
  - ggvenn_pq
  - graph_test_pq
  - LCBD_pq
  - multi_biplot_pq
  - plot_LCBD_pq
  - plot_SCBD_pq
  - plot_tsne_pq
  - ridges_pq
  - SRS_curve_pq
  - tsne_pq
  - umap_pq
  - upset_pq
  - upset_test_pq
  - var_par_pq
  - var_par_rarperm_pq
  - plot_var_part_pq
  - venn_pq

- subtitle: Differential abundance analysis
  contents:
  - multipatt_pq
  - phyloseq_to_edgeR
  - plot_edgeR_pq
  - plot_deseq2_pq
  - plot_mt
  - ancombc_pq
  - signif_ancombc
  - plot_ancombc_pq

- subtitle: Taxonomy
  contents:
  - ggaluv_pq
 #- heat_tree_pq
  - krona
  - merge_krona
  - multitax_bar_pq
  - physeq_or_string_to_dna
  - plot_guild_pq
  - plot_tax_pq
  - rotl_pq
  - sankey_pq
  - search_exact_seq_pq
  - tax_bar_pq
  - tax_datatable
  - treemap_pq
  - vs_search_global

- subtitle: Zoom on given taxa
  contents:
  - distri_1_taxa
  - taxa_only_in_one_level

- title: Improve reproducibility using [targets](https://books.ropensci.org/targets/) pipeline
- subtitle: Processing fastq files
  contents:
  - list_fastq_files
  - filter_trim
  - cutadapt_remove_primers
  - subsample_fastq
- subtitle: Import/export phyloseq object
  contents:
  - read_pq
  - save_pq
  - write_pq
- subtitle: Track info along pipeline
  contents:
  - count_seq
  - track_wkflow
  - track_wkflow_samples
- subtitle: Sample data management
  contents:
  - rename_samples_otu_table
  - rename_samples
  - sample_data_with_new_names
  - psmelt_samples_pq
- subtitle: Taxonomy management
  contents:
  - simplify_taxo
  - reorder_taxa_pq

- title: Datasets
  contents:
  - data_fungi
  - data_fungi_sp_known
  - data_fungi_mini
  - Tengeler2020_pq

- title: Other utilities
- subtitle: Color management
  contents:
  - funky_color
  - fac2col
  - transp
- subtitle: File management
  contents:
  - get_file_extension
- subtitle: External software management
  contents:
  - is_cutadapt_installed
  - is_falco_installed
  - is_krona_installed
  - is_mumu_installed
  - is_swarm_installed
  - is_vsearch_installed
- subtitle: Plot management
  contents:
  - multiplot
  - no_legend
- subtitle: Variable management
  contents:
  - diff_fct_diff_class
  - perc
  - unique_or_na
- subtitle: Others
  contents:
  - all_object_size
  - dist_bycol
  - dist_pos_control
  - are_modality_even_depth
  - MiscMetabar-package

- title: Deprecated
  contents:
  - adonis_phyloseq
  - biplot_physeq
  - clean_physeq
  - ggVenn_phyloseq
  - hill_phyloseq
  - hill_tuckey_phyloseq
  - lulu_phyloseq
  - otu_circle
  - physeq_graph_test
#  - physeq_heat_tree
  - plot_deseq2_phyloseq
  - plot_edgeR_phyloseq
  - read_phyloseq
  - sankey_phyloseq
  - summary_plot_phyloseq
  - venn_phyloseq
  - write_phyloseq


development:
  mode: auto