_pkgdown.yml

url: https://plant-food-research-open.github.io/moiraine/
template:
  bootstrap: 5
  bootswatch: zephyr
  bslib:
    font-size-sm: 1.1rem
    light: "#80acff"

navbar:
  bg: light
  title: targets
  type: default
  left:
  - text: Overview
    href: https://plant-food-research-open.github.io/moiraine-manual/overview.html
  - text: Reference
    href: reference/index.html
  - text: Manual
    href: https://plant-food-research-open.github.io/moiraine-manual/
  - text: News
    href: news/index.html
  right:
  - icon: fa-github fa-lg
    href: https://github.com/Plant-Food-Research-Open/moiraine

reference:
- title: "Project management"
  desc: "Getting started with a new data integration project"
  contents:
  - create_moiraine_pipeline

- title: "Data import"
  desc: "Importing data into R"
  contents:
  - import_dataset_csv
  - import_fmetadata_csv
  - import_fmetadata_gff
  - import_smetadata_csv
  - import_dataset_csv_factory
  - import_fmetadata_csv_factory
  - import_fmetadata_gff_factory
  - import_smetadata_csv_factory

- title: "Omics and multi-omics sets creation"
  desc: "Creating omics sets"
  contents:
  - create_omics_set
  - create_omics_set_factory
  - create_multiomics_set
  - add_omics_set
  - MetabolomeSet
  - PhenotypeSet
  - add_metabo
  - add_pheno

- title: "Multi-omics sets (MultiDataSet objects)"
- subtitle: "Querying"
  desc: "Querying the MultiDataSet object"
  contents:
  - n_features
  - n_samples
  - get_features
  - get_samples
  - get_datasets
  - get_dataset_matrix
  - get_features_metadata
  - get_samples_metadata
  - get_samples_metadata_combined
  - check_missing_values
  - get_features_labels
  - join_features_metadata
  - join_samples_metadata
- subtitle: "Plotting"
  desc: "Plotting properties of omics datasets"
  contents:
  - plot_samples_upset
  - plot_density_data
  - plot_meansd_data
  - plot_data_covariate
  - plot_data_heatmap
- subtitle: "Modifying"
  desc: "Modifying or subsetting datasets or metadata"
  contents:
  - replace_dataset
  - round_dataset
  - add_features_metadata
  - add_samples_metadata
  - subset_features

- title: "PCA"
  desc: "PCA and missing values imputation on multi-omics set"
  contents:
  - run_pca
  - run_pca_matrix
  - get_complete_data
  - pca_complete_data_factory
  - plot_screeplot_pca
  - plot_samples_coordinates_pca
  - get_pca_arguments

- title: "Transformation"
  desc: "Omics datasets transformation and normalisation"
  contents:
  - starts_with("transform_")
  - transformation_datasets_factory
  - get_transformed_data
  - get_table_transformations
  - zero_to_half_min

- title: "Prefiltering"
  desc: "Features prefiltering for multi-omics set"
- subtitle: "Unsupervised (Median Absolute Variation)"
  contents:
  - select_features_mad
  - select_features_cov
  - select_features_mad_matrix
  - select_features_cov_matrix
  - get_filtered_dataset_variability
  - feature_preselection_mad_factory
  - feature_preselection_cov_factory
  - plot_feature_preselection_mad
  - plot_feature_preselection_cov
- subtitle: "Supervised (sPLS-DA)"
  contents:
  - get_input_splsda
  - perf_splsda
  - run_splsda
  - get_filtered_dataset_splsda
  - feature_preselection_splsda_factory
  - plot_feature_preselection_splsda

- title: "Supervised integration"
  desc: "Integration of datasets aiming to discriminate samples based on an outcome of interest"
- subtitle: "DIABLO"
  desc: "Supervised integration with the DIABLO method from mixOmics"
  contents:
  - get_input_mixomics_supervised
  - run_pairwise_pls
  - starts_with("diablo_")
- subtitle: "MEFISTO"
  desc: "Supervised integration with the MEFISTO method from MOFA2 (for time-series or spatially resolved data)"
  contents:
  - get_input_mefisto

- title: "Unsupervised integration"
  desc: "Integration of datasets aiming at assessing variation common to the datasets"
- subtitle: "MOFA"
  desc: "Unsupervised integration with the MOFA method from MOFA2"
  contents:
  - get_input_mofa2
  - get_input_mofa
  - starts_with("mofa_")

- subtitle: "sO2PLS"
  desc: "Unsupervised integration of 2 datasets with the sO2PLS method from omicsPLS"
  contents:
  - get_input_omicspls
  - starts_with("so2pls_")
- subtitle: "sPLS"
  desc: "Unsupervised integration of 2 datasets with the sPLS method from mixOmics"
  contents:
  - get_input_spls
  - get_input_mixomics_unsupervised
  - starts_with("spls_")

- title: "Standardised method output"
  desc: "Functions to get and query the results of an integration method as a standardised R object"
  contents:
  - get_output
  - get_latent_dimensions
  - get_top_features
  - get_selected_features
- subtitle: "Plotting functions"
  contents:
  - plot_variance_explained
  - plot_samples_score
  - plot_samples_score_pair
  - plot_samples_score_covariate
  - plot_features_weight_distr
  - plot_features_weight_pair
  - plot_features_weight_covariate
  - plot_top_features

- title: "Methods evaluation"
  desc: "Evaluating the results of an integration method against prior knowledge"
  contents:
  - evaluate_feature_selection_table
  - make_feature_sets_from_df
  - make_feature_sets_from_fm
  - check_feature_sets
  - reduce_feature_sets_data
  - evaluate_method_enrichment
  - plot_features_weight_set
  - compute_samples_silhouette

- title: "Methods comparison"
  desc: "Comparison of the results from several integration methods"
  contents:
  - get_samples_score_correlation
  - get_features_weight_correlation
  - starts_with("comparison")
  - compute_consensus_importance
  - consensus_importance_metric
  - show_consensus_metrics

- title: "Other (utils)"
  desc: "Other miscellaneous functions"
- subtitle: "Helper MultiDataSet object"
  contents:
  - check_is_multidataset
  - check_input_multidataset
- subtitle: "Helper plotting functions"
  contents:
  - plot_correlation_matrix
  - plot_correlation_matrix_full
  - ggpairs_custom
  - plot_x_wrapper
  - plot_x_continuous
  - plot_x_discrete
- subtitle: "Misc."
  contents:
  - hclust_matrix_rows
  - options_list_as_tibble
  - is_equal_or_null
- title: internal
  contents:
  - '`add_metabo,MultiDataSet,MetabolomeSet-method`'
  - '`add_pheno,MultiDataSet,PhenotypeSet-method`'
  - starts_with("\\.")