Merge branch 'malariagen:master' into remove_pf9_functionality

Author: nw20

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 <https://www.malariagen.net/data>`_ 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

docs/source/_static/images/anopheles_darlingi.jpg

@@ -66,6 +66,13 @@ API documentation
          :align: center
          :width: 100%
 
+   .. grid-item-card:: ``Adar1``
+      :link: Adar1
+      :link-type: doc
+
+      *Anopheles darlingi*
+      .. image:: ./_static/images/anopheles_darlingi.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.

docs/source/index.rst

@@ -152,7 +152,7 @@ def __repr__(self):
             f"Please note that data are subject to terms of use,\n"
             f"for more information see https://www.malariagen.net/data\n"
             f"or contact support@malariagen.net. For API documentation see \n"
-            f"https://malariagen.github.io/malariagen-data-python/v{malariagen_data.__version__}/Adir1.html"
+            f"https://malariagen.github.io/malariagen-data-python/v{malariagen_data.__version__}/Adar1.html"
         )
         return text
 
@@ -167,7 +167,7 @@ def _repr_html_(self):
                         Please note that data are subject to terms of use,
                         for more information see <a href="https://www.malariagen.net/data">
                         the MalariaGEN website</a> or contact support@malariagen.net.
-                        See also the <a href="https://malariagen.github.io/malariagen-data-python/v{malariagen_data.__version__}/Adir1.html">Adir1 API docs</a>.
+                        See also the <a href="https://malariagen.github.io/malariagen-data-python/v{malariagen_data.__version__}/Adar1.html">Adar1 API docs</a>.
                     </td></tr>
                 </thead>
                 <tbody>

malariagen_data/adar1.py

@@ -9,8 +9,7 @@ class Pf8(PlasmodiumDataResource):
     Parameters
     ----------
     url : str, optional
-        Base path to data. Default uses Sanger S3 Storage "s3://pf8-release/".
-        Alternative access through Google Cloud Storage "gs://pf8-release/" which requires authentication (https://malariagen.github.io/parasite-data/cloud_data_access/parasite-cloud-data-access.html#),
+        Base path to data. Default uses Google Cloud Storage "gs://pf8-release/" which requires authentication (https://malariagen.github.io/parasite-data/cloud_data_access/parasite-cloud-data-access.html#),
         or specify a local path on your file system if data have been downloaded.
     data_config : str, optional
         Path to config for structure of Pf8 data resource. Defaults to config included
@@ -20,7 +19,7 @@ class Pf8(PlasmodiumDataResource):
 
     Examples
     --------
-    Access data from Sanger S3 Storage (default):
+    Access data from Google Cloud Storage (default):
 
         >>> import malariagen_data
         >>> pf8 = malariagen_data.Pf8()