_pkgdown.yml

url: https://mskcc-epi-bio.github.io/gnomeR/

template:
  bootstrap: 5
  bootswatch: simplex
  bslib:
    primary: "#CC133C"
    base_font: {google: "Atkinson Hyperlegible"}
    heading_font: {google: "Atkinson Hyperlegible"}
    text-muted: "#FFFFFF"

authors:
  Karissa Whiting:
    href: "https://www.karissawhiting.com/"
  Jessica Lavery:
    href: "https://github.com/jalavery/"
  Mike Curry:
    href: "https://github.com/michaelcurry1123/"
  Hannah Fuchs:
    href: "https://github.com/hfuchs5/"

navbar:
  bg: primary
  structure:
    left:  [reference, articles, news]
    right: [search, github]

reference:
  - subtitle: Processing Data
  - contents:
    - create_gene_binary
    - summarize_by_gene
    - summarize_by_patient
    - pivot_cna_wider
    - pivot_cna_longer
    - add_pathways
    - recode_alias
    - reformat_fusion
    - subset_by_panel
  - subtitle: Analyzing Data
  - contents:
    - tbl_genomic
    - mutation_viz
    - ggvarclass
    - ggvartype
    - ggsamplevar
    - ggtopgenes
    - gggenecor
    - ggcomut
    - subset_by_frequency
  - subtitle: Helper Functions
  - contents:
    - which_impact_panel
    - recode_cna
    - rename_columns
    - resolve_alias
    - extract_patient_id
  - subtitle: Color Palette
  - contents:
    - gnomer_colors
    - gnomer_palettes
    - gnomer_palette
    - set_gnomer_palette
    - reset_gnomer_palette
  - subtitle: Example Data Sets
  - contents:
    - mutations
    - cna
    - sv
    - seg
    - cna_wide
    - consequence_map
    - gene_panels
    - names_df
    - pathways
    - impact_alias_table
    - genie_alias_table
    - sv_long
    - clin_collab_df
    - genie_mut
    - genie_cna
    - genie_fusion