Jupyter Widget API Documentation

bdgenomics.mango.pileup Package

Each widget instance calls the PileupViewer to draw an interactive widget for genomic data.

PileupViewer

PileupViewer(**kwargs) Widget wrapper for pileup.js viewer in Jupyter notebooks.

Sources

Sources specify where the genomic data comes from. Sources can come from a url, a GA4GHDatasource, or a JSON string of GA4GH formatted data.

BamDataSource(url[, indexUrl]) Initializes file source from bam file endpoint.
VcfDataSource(url[, indexUrl]) Initializes file source from vcf file endpoint.
TwoBitDataSource(url[, indexUrl]) Initializes file source from twoBit file endpoint.
BigBedDataSource(url[, indexUrl]) Initializes file source from big bed (.bb) file endpoint.
GA4GHAlignmentJson(json) Initializes GA4GH Alignment JSON.
GA4GHVariantJson(json) Initializes GA4GH variant JSON.
GA4GHFeatureJson(json) Initializes GA4GH feature JSON.
GA4GHAlignmentSource(endpoint, readGroupId) Initializes GA4GHAlignmentSource.
GA4GHVariantSource(endpoint, readGroupId[, …]) Initializes GA4GHSource.
GA4GHFeatureSource(endpoint, readGroupId[, …]) Initializes GA4GHFeatureSource.

Track

Tracks specify what visualization will be drawn.

Track(**kwargs) A trait for a pileupTrack, requires a viz string of (coverage, pileup, features, variants, genome, genes, scale, or location) and a DataSource.
track_to_json(pyTrack, manager) Serialize a Track.
track_from_json(js, manager) Deserialize a Track from JSON.
tracks_to_json(pyTracks, manager) Serialize a Python date object.
tracks_from_json(js, manager) Deserialize a list of Tracks from JSON.