Merge pull request #839 from malariagen/amin1.0-clean

Clean Amin1.0 branch from master

Author: tristanpwdennis

docs/source/Amin1.rst

@@ -15,11 +15,20 @@ All the functions below can then be accessed as methods on the ``amin1`` object.
     df_samples = amin1.sample_metadata()
 
 For more information about the data and terms of use, please see the
-`MalariaGEN Vector Observatory Asia <https://www.malariagen.net/mosquito/vector-observatory-asia>`_
-home page.
+`MalariaGEN website <https://www.malariagen.net/data>`_ or contact support@malariagen.net.
 
 .. currentmodule:: malariagen_data.amin1.Amin1
 
+Basic data access
+-----------------
+.. autosummary::
+    :toctree: generated/
+
+    releases
+    sample_sets
+    lookup_release
+    lookup_study
+
 Reference genome data access
 ----------------------------
 .. autosummary::
@@ -28,17 +37,114 @@ Reference genome data access
     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