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. |