_pkgdown.yml

url: https://mjs-708.github.io/quantMSImageR/

# Figure numbering: the vignettes render through BiocStyle, which numbers
# figures ("Figure 1: ..."). pkgdown re-renders them with its own output format
# and drops that, so captions here are unnumbered while the Bioconductor-built
# vignettes are numbered. Setting `pkgdown: as_is: true` in the vignette headers
# restores BiocStyle, but its output carries no pkgdown navbar and
# build_articles() then dies in activate_navbar(). Left as is deliberately.

template:
  bootstrap: 5
  bslib:
    primary: "#0f8096"

home:
  title: Processing and quantification of targeted mass spectrometry imaging data
  links:
  - text: Read the paper
    href: https://doi.org/10.1021/acs.analchem.4c02350

navbar:
  structure:
    left:  [intro, reference, articles]
    right: [search, github]

# Grouped by the @family tags used in the roxygen blocks, in pipeline order:
# read an acquisition, assemble several, filter, visualise, quantify. An
# alphabetical index would separate functions that are only meaningful together.
reference:
- title: Acquisition
  desc: >
    Reading a `.raw` folder against an ion library, labelling tissue against
    background, and trimming what is not wanted.
  contents:
  - read_mrm
  - select_tissue_pixels
  - trim_MSI
  - remove_blank_mzs
  - build_feature_meta

- title: Combining acquisitions
  desc: >
    Putting several acquisitions, or the two polarities of one acquisition,
    into a single object.
  contents:
  - align_features
  - combine_MSIs
  - bind_panels
  - stitch_acquisitions

- title: Filtering and normalisation
  desc: >
    Internal-standard response, background-referenced signal, and the masking
    steps that act on a chosen spectra layer.
  contents:
  - int2response
  - int2snr
  - applySNR
  - back2NA
  - zero2na

- title: Quantification
  desc: >
    Standards to a fitted model to an estimated amount per pixel, plus the
    coverage check that says whether the standards bracket the tissue.
  contents:
  - summarise_cal_levels
  - create_cal_curve
  - int2conc
  - plot_cal_coverage

- title: Visualisation
  contents:
  - imageR
  - quantile_hm
  - contribution_hm
  - quant_palettes

- title: Whole-study workflows
  desc: >
    Running a complete study from a YAML configuration, and the worked example.
  contents:
  - run_study
  - validate_config
  - print.quant_validation
  - generate_txt_images
  - run_example

- title: Classes and accessors
  desc: >
    The `quant_MSImagingExperiment` object and the calibration and tissue
    metadata it carries.
  contents:
  - quant_MSImagingExperiment
  - calibrationInfo-class
  - tissueInfo-class
  - quantMSImageR-accessors
  - createMSIDatamatrix

- title: Package
  contents:
  - quantMSImageR-package

articles:
- title: Vignettes
  navbar: ~
  contents:
  - quantMSImageR
  - quantification