_pkgdown_old.yml

destination: docs

template:
  params:
    part_of: evoverse
    footer: S. Milite and G. Caravagna.
url:
  militeee.github.io/Rcongas

repo:
  url:
    home: https://github.com/militeee/Rcongas/
    source: https://github.com/militeee/Rcongas
    issue: https://github.com/militeee/Rcongas/issues
    user: https://github.com/militeee

navbar:
 components:
   articles:
    text: Articles
    menu:
    - text: Models
      href: articles/1_Models.html
    - text: Models 
      href: articles/2_Models.html
    - text: Getters
      href: articles/3_Getters.html
    - text: Plotting functions
      href: articles/4_Plotting_functions.html
    - text: Preprocessing
      href: articles/5_Preprocessing.html


authors:
  Salvatore Milite:
    href: https://sites.google.com/view/cdslab
  Giulio Caravagna:
    href: https://sites.google.com/view/cdslab

reference:
- title: Available data
  desc:  Data released with the package
  contents:
  - congas_example

- title: Fitting functions
  desc:  Functions to cluster the data.
  contents:
  - approx_theta_prior_params
  - best_cluster
  - list_models
  - recalculate_information_criteria
  - run_inference

- title: S3 functions
  desc: The `rcongas` S3 object.
  contents:
  - print.rcongas
  - summary.rcongas
  - plot.rcongas

- title: Plotting functions
  desc:  Functions to plot data and fits.
  contents:
  - plot_chromosome
  - plot_gw_cna_profiles
  - plot_inference_report
  - plot_counts_rna_segments
  - plot_raw_data
  - plot_highlights
  - plot_latent_variables
  - plot_mixing_proportions
  - plot_normalization_factors
  - plot_segment_density
  - report_analysis

- title: Getters for clustering results
  desc:  Functions to extract clustering information from a model.
  contents:
  - get_clusters
  - get_clusters_ploidy
  - get_clusters_size
  - get_k
  - get_segment_test_counts

- title: Getters for input data
  desc:  Functions to extract information of the data stored in a model.
  contents:
  - get_counts
  - get_input_segmentation
  - get_mapped_genes
  - get_input_raw_data
  - get_reference_genome
  - get_gene_annotations
  - get_dataset_stats
  - get_segment_ids
  - get_model_description
  
- title: Filter functions
  desc:  Functions to filter out information from a model.
  contents:
  - filter_clusters

  
- title: Synthetic data generation functions
  desc:  Functions to sample from the generative model.
  contents:
  - generate_random_tree
  - run_simulation


- title: Other analyses (DE, GSE)
  desc:  Differential Expression, Gene Set Enrichment, etc.
  contents:
  - calculate_DE
  - get_DE_table
  - plot_DE_gw
  - plot_DE_volcano