_pkgdown.yml

url: https://samuel-marsh.github.io/scCustomize/

template:
  params:
      bootswatch: flatly

home:
  sidebar:
    structure: [links, license, custom, authors, dev]
    components:
      custom:
        title: Citation
        text: "[Citing scCustomize](https://samuel-marsh.github.io/scCustomize/articles/FAQ.html)"

navbar:
  left:
    - text: "Getting Started"
      href: index.html
    - text: "Install"
      href: articles/Installation.html
    - text: "Vignettes"
      menu:
        - text: Plotting Vignettes
        - text: "Plotting #1: General Analysis Plots"
          href: articles/Gene_Expression_Plotting.html
        - text: "Plotting #2: QC Plots & Analysis"
          href: articles/QC_Plots.html
        - text: "Plotting #3: Sequencing QC Plots/Analysis"
          href: articles/Sequencing_QC_Plots.html
        - text: "Plotting #4: Iterative Plotting Functions"
          href: articles/Iterative_Plotting.html
        - text: "Plotting #5: Spatial Plotting Functions"
          href: articles/Spatial_Plotting.html
        - text: "Customized Color Palettes & Themes"
          href: articles/Color_Palettes.html
        - text: -------
        - text: Helpers & Utilities
        - text: "General Helpers & Utilities"
          href: articles/Helpers_and_Utilities.html
        - text: "Object QC Functions"
          href: articles/Object_QC_Functions.html
        - text: "Read & Write Data Functions"
          href: articles/Read_and_Write_Functions.html
        - text: "Object/Assay Format Conversion"
          href: articles/Object_Conversion.html
        - text: "Marker Identification & Cluster Annotation Helpers"
          href: articles/Markers_and_Cluster_Annotation.html
        - text: "Statistics Functions"
          href: articles/Statistics.html
        - text: "Updating Gene Symbols"
          href: articles/Update_Gene_Symbols.html
        - text: "Misc Functions"
          href: articles/Misc_Functions.html
        - text: -------
        - text: Other Package Interactivity/Functions
        - text: "LIGER Plotting & Functionality"
          href: articles/LIGER_Functions.html
        - text: "Cell Bender Functionality & Plotting"
          href: articles/Cell_Bender_Functions.html
    - text: "News/Changelog"
      href: news/index.html
    - text: "Reference"
      href: reference/index.html
    - text: FAQ
      href: articles/FAQ.html

reference:
- title: "Read & Write Data"
  desc: "Functions for reading and writing single cell sequencing data from raw data files."
- contents:
  - has_concept("read_&_write")
- subtitle: "Merge Data Utilities"
  desc: "Utilities to merge raw data."
- contents:
  - has_concept("read_merge_util")
- subtitle: "Edit Barcode Utilities"
  desc: "Utilities to edit cell barcodes"
- contents:
  - has_concept("barcode_util")

- title: "Sequencing Metrics QC Plots"
  desc: "Functions plotting various QC metrics provides by 10X Genomics Cell Ranger Outputs"
- contents:
  - has_concept("seq_qc_plotting_layout")
  - has_concept("seq_qc_plotting_basic")
  - has_concept("seq_qc_plotting_alignment")

- title: "Basic Analysis QC Plots"
  desc: "Functions plotting various QC from Seurat Objects."
- contents:
  - has_concept("object_qc_plotting")

- title: "Seurat Plotting Functions"
  desc: "Functions customization and plotting of single cell data/results from Seurat Objects."
- contents:
  - has_concept("seurat_plotting")
  - has_concept("other_seurat_plotting")

- title: "Iterative Plotting Functions"
  desc: "Functions for quick iterative plotting."
- contents:
  - has_concept("iterative_plotting")

- title: "LIGER Plotting Functions"
  desc: "Functions customization and plotting of single cell data/results from LIGER Objects."
- contents:
  - has_concept("liger_plotting")

- title: "Plotting Utilities #1 (Color Palettes)"
  desc: "Helper functions for quick access to useful or default color palettes."
- contents:
  - has_concept("palettes")

- title: "Plotting Utilities #2 (Themes/Theme Adjustment)"
  desc: "Helper functions for quick modification of theme elements and custom themes."
- contents:
  - has_concept("themes")

- title: "Helper Utilities (Seurat)"
  desc: "Functions to provide ease of use for frequently used code from Seurat Objects."
- subtitle: "QC Utilities"
  desc: "Functions to add common QC variables to meta.data."
- contents:
  - has_concept("qc_util")
- subtitle: "Getters/Setters"
  desc: "Functions to extract data from or add additional data to Seurat objects"
- contents:
  - has_concept("get_set_util")
- subtitle: "Check Utilities"
  desc: "Functions to check validity of different aspects of object or object contents."
- contents:
  - has_concept("check_util")
- subtitle: "Misc Utilities"
  desc: "Miscellaneous Utilities"
- contents:
  - has_concept("misc_util")

- title: "Helper Utilities (LIGER)"
  desc: "Functions to provide ease of use for frequently used code from LIGER Objects."
- contents:
  - has_concept("liger_object_util")

- title: "Object Conversion Functions"
  desc: "Functions to convert between different single cell object formats (R & Python)."
- contents:
  - has_concept("object_conversion")

- title: "Cluster/Marker Annotation Utilities"
  desc: "Functions to provide ease of use or add functionality to DEG and cluster annotation."
- contents:
  - has_concept("marker_annotation_util")

- title: "Project Organization Utilities"
  desc: "Functions to provide ease of use for organization of analysis projects."
- contents:
  - has_concept("organization_util")

- title: "Statistics Functions"
  desc: "Functions quick return of different object and data metrics."
- contents:
  - has_concept("stats")
  - has_concept("stats_plotting")

- title: "Data"
  desc: "Reference data for package functions."
- contents:
  - has_concept("data")

deploy:
  install_metadata: true