_pkgdown.yml

template:
  params:
    part_of: evoverse
    footer: Test of my footer
url:
  caravagnalab.github.io/revolver
  
# articles:
# - title: R Markdown
#   contents:
#   - starts_with("authoring")
# - title: Websites
#   contents:
#   - rmarkdown_websites
#   - rmarkdown_site_generators

  
authors:
  Giulio Caravagna:
    href: https://www.caravagnalab.org/

reference:
- title: Cohort functions
  desc:  These functions can be used to create or modify a REVOLVER cohort and its trees.
  contents:
  - revolver_cohort
  - revolver_check_cohort
  - compute_clone_trees
  - compute_mutation_trees
  - input_custom_trees
  - CCF_parser
  - remove_drivers
  - remove_patients
  
- title: Analysis functions
  desc:  These functions can be used to analyse a REVOLVER cohort.
  contents:
  - revolver_fit
  - revolver_cluster
  - revolver_jackknife
  
- title: Getters functions
  desc:  These functions can be used to extract data from a REVOLVER cohort object. These include the raw data used to create the cohort, driver information, clonal and subclonal events, the trees that are associated to the patients and other analysis results.
  contents:
  - Data
  - Drivers
  - Truncal
  - Subclonal
  - Samples
  - Clonal_cluster
  - CCF
  - CCF_clusters
  - Phylo
  - ITransfer
  - get_features
  - Cluster
  - Jackknife_patient_coclustering
  - Jackknife_cluster_stability
  - Jackknife_trajectories_stability
  
- title: Stats functions
  desc:  These functions can be used to extract either cohort-level statistics data from a REVOLVER cohort object, and other statistics that regard the computations performed on the cohort.
  contents:
  - starts_with("Stats")
  - DET_index
  
- title: Plotting functions
  desc:  These functions can be used to plot data, fits and clusters from a REVOLVER cohort object.
  contents:
  - starts_with("plot_")
  - distinct_palette_few
  - distinct_palette_many
  - gradient_palette
  
- title: S3 functions
  desc:  The two S3 classes of REVOLVER objects implement the following S3 mehtods. Class `rev_cohort` represents a basic cohort object before the fits, class `rev_cohort_fit` is a cohort object where fits are now available.
  contents:
  - print.rev_cohort
  - print.rev_cohort_fit
  - plot.rev_cohort
  - plot.rev_cohort_fit