diff --git a/docs/source/Adar1.rst b/docs/source/Adar1.rst new file mode 100644 index 000000000..935a0f895 --- /dev/null +++ b/docs/source/Adar1.rst @@ -0,0 +1,141 @@ +Adar1 +===== + +This page provides a curated list of functions and properties available in the ``malariagen_data`` API +for data on mosquitoes from the *Anopheles darlingi* complex. + +To set up the API, use the following code:: + + import malariagen_data + adar1 = malariagen_data.Adar1() + +All the functions below can then be accessed as methods on the ``adar1`` object. E.g., to call the +``sample_metadata()`` function, do:: + + df_samples = adar1.sample_metadata() + +For more information about the data and terms of use, please see the +`MalariaGEN website `_ or contact support@malariagen.net. + +.. currentmodule:: malariagen_data.adar1.Adar1 + +Basic data access +----------------- +.. autosummary:: + :toctree: generated/ + + releases + sample_sets + lookup_release + lookup_study + +Reference genome data access +---------------------------- +.. autosummary:: + :toctree: generated/ + + contigs + genome_sequence + genome_features + plot_transcript + plot_genes + +Sample metadata access +---------------------- +.. autosummary:: + :toctree: generated/ + + sample_metadata + add_extra_metadata + clear_extra_metadata + lookup_sample + count_samples + plot_samples_bar + plot_samples_interactive_map + plot_sample_location_mapbox + plot_sample_location_geo + wgs_data_catalog + cohorts + +SNP data access +--------------- +.. autosummary:: + :toctree: generated/ + + site_mask_ids + snp_calls + snp_allele_counts + plot_snps + is_accessible + biallelic_snp_calls + biallelic_diplotypes + biallelic_snps_to_plink + +SNP frequency analysis +---------------------- +.. autosummary:: + :toctree: generated/ + + snp_allele_frequencies + snp_allele_frequencies_advanced + aa_allele_frequencies + aa_allele_frequencies_advanced + plot_frequencies_heatmap + plot_frequencies_time_series + plot_frequencies_interactive_map + +Principal components analysis (PCA) +----------------------------------- +.. autosummary:: + :toctree: generated/ + + pca + plot_pca_variance + plot_pca_coords + plot_pca_coords_3d + +Genetic distance and neighbour-joining trees (NJT) +-------------------------------------------------- +.. autosummary:: + :toctree: generated/ + + plot_njt + njt + biallelic_diplotype_pairwise_distances + +Heterozygosity analysis +----------------------- +.. autosummary:: + :toctree: generated/ + + plot_heterozygosity + roh_hmm + plot_roh + +Diversity analysis +------------------ +.. autosummary:: + :toctree: generated/ + + cohort_diversity_stats + diversity_stats + plot_diversity_stats + +Diplotype clustering +-------------------- +.. autosummary:: + :toctree: generated/ + + plot_diplotype_clustering + plot_diplotype_clustering_advanced + +Fst analysis +------------ +.. autosummary:: + :toctree: generated/ + + average_fst + pairwise_average_fst + plot_pairwise_average_fst + fst_gwss + plot_fst_gwss diff --git a/docs/source/index.rst b/docs/source/index.rst index fd277170a..dea8d1b0c 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -66,6 +66,13 @@ API documentation :align: center :width: 100% + .. grid-item-card:: ``Adar1`` + :link: Adar1 + :link-type: doc + + *Anopheles darlingi* + .. image:: https://en.wikipedia.org/wiki/File:Bioswiki.jpg + Documentation for the `Pf7 `_ (*Plasmodium falciparum*) and `Pv4 `_ (*Plasmodium vivax*) APIs is also available, currently hosted on a separate site.