Merge pull request #795 from malariagen/adir1.x

Adir1.x

Author: jonbrenas

docs/source/Adir1.rst

@@ -0,0 +1,150 @@
+Adir1
+=====
+
+This page provides a curated list of functions and properties available in the ``malariagen_data`` API
+for data on mosquitoes from the *Anopheles dirus* complex.
+
+To set up the API, use the following code::
+
+    import malariagen_data
+    adir1 = malariagen_data.Adir1()
+
+All the functions below can then be accessed as methods on the ``adir1`` object. E.g., to call the
+``sample_metadata()`` function, do::
+
+    df_samples = adir1.sample_metadata()
+
+For more information about the data and terms of use, please see the
+`MalariaGEN website <https://www.malariagen.net/data>`_ or contact support@malariagen.net.
+
+.. currentmodule:: malariagen_data.adir1.Adir1
+
+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
+    site_annotations
+    is_accessible
+    biallelic_snp_calls
+    biallelic_diplotypes
+    biallelic_snps_to_plink
+
+Integrative genomics viewer (IGV)
+---------------------------------
+.. autosummary::
+    :toctree: generated/
+
+    igv
+    view_alignments
+
+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

docs/source/index.rst

@@ -35,6 +35,14 @@ API documentation
 
       .. image:: https://upload.wikimedia.org/wikipedia/commons/thumb/1/11/Anopheles_minimus_1.jpg/640px-Anopheles_minimus_1.jpg
 
+   .. grid-item-card:: ``Adir1``
+      :link: Adir1
+      :link-type: doc
+
+      *Anopheles dirus* complex.
+
+      .. image:: https://phil.cdc.gov//PHIL_Images/8777/8777_lores.jpg
+
 Documentation for the `Pf7 <https://malariagen.github.io/parasite-data/pf7/api.html>`_ (*Plasmodium falciparum*)
 and `Pv4 <https://malariagen.github.io/parasite-data/pv4/api.html>`_ (*Plasmodium vivax*) APIs is also available,
 currently hosted on a separate site.

malariagen_data/__init__.py

@@ -1,4 +1,5 @@
 # flake8: noqa
+from .adir1 import Adir1
 from .af1 import Af1
 from .ag3 import Ag3
 from .amin1 import Amin1