mkdocs.yml

site_name: GWASLab
site_author: HE Yunye
repo_name: 'GitHub'
repo_url: https://github.com/Cloufield/gwaslab/
edit_uri: ""
copyright: "GWASLab is licensed under the MIT license"
theme:
  name: material
  features:
    - navigation.tabs
  font:
    code: Roboto Mono
    text: Roboto
  palette:
    primary: blue
    accent: blue
  logo: assets/gwaslab.png
  favicon: assets/gwaslab.png
    
nav:
    - Home:
       - Home : index.md
       - "Update logs" : UpdateLogs.md
       - "Known Issues" : KnownIssues.md
       - "Reserved Headers": reserved_header.md
    - Tutorial: tutorial.ipynb
    - Sumstats manipulation:
       - "Sumstats Object": SumstatsObject.md
       - "Status Code": StatusCode.md
       - "Standardization and Normalization": Standardization.md
       - "QC and Filtering": QC&Filtering.md
       - Harmonization: Harmonization.md
       - "Assigning rsID" : AssignrsID.md
       - "Assign CHR/POS using rsID" : AssignCHRPOS.md
       - Liftover: LiftOver.md
       - "Data conversion": Conversion.md
    - Visualization:
       - "Manhattan and QQ plot": Visualization.md
       - "Regional Plot": RegionalPlot.md
       - "Brisbane Plot": BrisbanePlot.md
       - "Miami Plot": MiamiPlot.md
       - "Trumpet Plot (testing)": TrumpetPlot.md
       - "Effect Size Comparison": EffectSize.md
       - "Allele Frequency Comparison": AlleleFrequency.md
       - "Genetic correlation heatmap" : GeneticCorrelation.md
       - "Gallery" : Gallery.md
    - Utilities: 
       - "Extract Lead Variants": ExtractLead.md
       - "Extract Novel Variants": ExtractNovel.md
       - "Format and Save": Format.md
       - "Save Sumstats Object": Pickle.md 
       - "Load LDSC log": LoadLDSC.md
       - "Convert Heritability": HeritabilityConversion.md
       - "Per-SNP R2 and F" : PerSNPh2.md
       - "Infer Genome Build": InferBuild.md
    - Downstream:
       - "LDSC in GWASLab": LDSCinGWASLab.md
    - References:
       - "Download": Download.md 
       - "Reference data" : Reference.md
       - "Common data": CommonData.md
       - "Hapmap3": Hapmap3.md
       - "HLA region": HLA.md
    - Examples:
       - "Standardization": standardization_workflow.ipynb
       - "Harmonization" : harmonization_workflow.ipynb
       - "Output sumstats" : format_load_save.ipynb
       - "Liftover" : harmonization_liftover.ipynb
       - "LD score regression" : ldsc_in_gwaslab.ipynb
       - "Lead and novel variants" : utility_get_lead_novel.ipynb
       - "Data conversion" : utility_data_conversion.ipynb
       - "Manhattan and QQ plot": visualization_mqq.ipynb     
       - "Regional plot" : visualization_regional.ipynb
       - "Miami plot": visualization_miami2.ipynb
       - "Stacked MQQ plot": visualization_stacked_mqq.ipynb
       - "Brisbane plot" : visualization_brisbane.ipynb
       - "Correlation heatmap" : visualization_plot_genetic_correlation.ipynb
       - "Download reference": Download_reference.ipynb


markdown_extensions:
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  - admonition
  - pymdownx.details
  - pymdownx.superfences
  - pymdownx.arithmatex:
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      line_spans: __span
      pygments_lang_class: true
  - pymdownx.inlinehilite
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  - pymdownx.superfences
  - tables

extra_javascript:
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  - https://polyfill.io/v3/polyfill.min.js?features=es6
  - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js
  - https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js
  - javascripts/tablesort.js

extra_css:
  - stylesheets/extra.css

plugins:
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  - search