As1.rst

As1

This page provides a curated list of functions and properties available in the malariagen_data API for data on Anopheles stephensi species mosquitoes.

To set up the API, use the following code:

import malariagen_data
as1 = malariagen_data.As1()

All the functions below can then be accessed as methods on the as1 object. E.g., to call the sample_metadata() function, do:

df_samples = as1.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.as1.As1

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