_pkgdown.yml

url: https://computational-metabolomics.github.io/MetMashR/
template:
  bootstrap: 5
  bootswatch: flatly
navbar: 
  type: standard
  left:
    - text: "Reference"
      href: reference/index.html
    - text: Articles
      menu:
      - text: Using MetMashR
        href: articles/using_MetMashR.html
      - text: Extending MetMashR
        href: articles/Extending_MetMashR.html
      - text: Annotating mixtures of standards
        href: articles/annotate_mixtures.html
      - text: Exploring the MTox700+ database
        href: articles/exploring_mtox.html
      - text: Processing Annotations for LCMS of Daphnia samples
        href: articles/daphnia_example.html
  right:
    - icon: fa-github
      href: https://github.com/computational-metabolomics/MetMashR
      aria-label: 'GitHub'
    - icon: fa-flask
      href: https://www.birmingham.ac.uk/research/activity/phenome-centre/index.aspx
      aria-label: 'Phenome Centre Birmingham'
    - icon: fa-music
      menu: 
      - text: MetMashR
        href: https://www.bioconductor.org/packages/release/bioc/html/MetMashR.html
      - text: struct
        href: https://www.bioconductor.org/packages/release/bioc/html/struct.html
      - text: structToolbox
        href: https://www.bioconductor.org/packages/release/bioc/html/structToolbox.html
      - text: metabolmicsWorkbenchR
        href: https://www.bioconductor.org/packages/release/bioc/html/metabolomicsWorkbenchR.html
      - text: pmp
        href: https://www.bioconductor.org/packages/release/bioc/html/pmp.html
reference:
- title: "Annotation sources"
  desc: >
    An `annotation source` is the dataset object used by all MetMashR objects.
    Different types of source have been defined, depending on the intended use
    of the data.
  contents:
  - ends_with('_source')
- title: "Annotation tables"
  desc: >
    Annotation tables represent the data imported from a source that includes
    experimentally measured data. Annotation tables are extended to support the
    specifics of an analytical platform used to collect the data.
  contents:
  - ends_with("_table")
- title: "Annotation databases"
  desc: >
    Annotation databases are (often remote) sources of annotation related 
    meta data, such as molecular identifiers, pathways etc.
  contents:
  - ends_with('_database')
  - rds_cache
  - github_file
  - is_writable
  - read_database
  - write_database
- title: "REST API interfaces"
  desc: >
    MetMashR includes a REST API object that has been extended to accomodate
    various services.
  contents:
  - rest_api
  - ends_with('_lookup')
- title: "Annotation table mashing"
  desc: >
    These models provide steps for cleaning, filtering, prioritising and 
    combining annotation tables from different sources.
  contents:
  - add_columns
  - add_labels
  - calc_ppm_diff
  - calc_rt_diff
  - prioritise_columns
  - combine_sources
  - vertical_join
  - combine_records
  - filter_labels
  - filter_range
  - filter_na
  - filter_venn
  - filter_records
  - id_counts
  - mz_match
  - rt_match
  - mzrt_match
  - normalise_lipids
  - normalise_strings
  - trim_whitespace
  - combine_columns
  - select_columns
  - remove_columns
  - split_column
  - split_records
  - AnnotationDb_select
  - compute_column
  - compute_record
  - pivot_columns
  - rename_columns
  - unique_records
- title: "Combining records"
  desc: >
    Combining records is an important step in the annotation mashing workflow.
    These functions can be used with the combine_records function to merge
    the information for multiple records in different ways.
  contents:
  - fuse
  - fuse_unique
  - count_records
  - compute_mean
  - compute_median
  - compute_mode
  - select_exact
  - select_grade
  - select_match
  - select_max
  - select_min
  - prioritise
  - nothing
- title: "Charts"
  desc: >
    Chart objects are wrappers around ggplot objects plots useful for exploring
    and visualising the information present in a table of annotations.
  contents:
    - ends_with('_structure')
    - ends_with('_chart')
    - annotation_histogram
    - annotation_histogram2d
    - pubchem_widget
- title: "BiocFileCache_database helper functions"
  desc: >
    These functions can be used with BiocFileCache_database objects to modify
    a dowloaded resource before caching, or to parse the downloaded resource
    when retrieved from the cache.
  contents:
  - cache_as_is
  - unzip_before_cache
- title: "Dictionaries for normalising strings"
  desc: >
    These lists define patterns and replacements to match when using the 
    normalise_strings object.
  contents:
  - ends_with('_dictionary')
- title: "Additional functions"
  desc: >
    Supporting functions are used by MetMashR
  contents:
  - check_for_columns
  - required_cols
  - wherever
  - chart_plot
  - model_apply
home:
  links:
  - text: View on Bioconductor
    href: https://bioconductor.org/packages/release/bioc/html/MetMashR.html