Package: igv-jupyterlab
igv-jupyterlabigv-jupyterlab is an extension for Jupyter Lab and traditional Jupyter Notebooks which wraps igv.js.InstallationYou can install usingpip:pipinstalligv_jupyterlabIf you are using Jupyter Notebook 5.2 or earlier, you may also need to enable
the nbextension:jupyternbextensionenable--py[--sys-prefix|--user|--system]igv_jupyterlabUsageThis extension provides a python wrapper which allows you render igv.js
in a cell and call its API from the notebook.InitializationTo insert an IGV instance into a cell:fromigv_jupyterlabimportIGV# At minimum, IGV requires a single argument, genome.# For supported genomes, a simple name may be supplied.IGV(genome="hg19")# For all other genomes, we must construct a configuration object.# A helper method supplied to make this easier.genome=IGV.create_genome(name="Human (GRCh38/hg38)",fasta_url="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa",index_url="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa.fai",cytoband_url="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg38/cytoBandIdeo.txt",)igv=IGV(genome=genome)display(igv)Supported genomes arelisted here.
Reference configuration is described in theigv.js documentation.# It is also easy to change the genome to something elsesome_other_genome=igv.create_genome(...)igv.load_genome(some_other_genome)TracksTo load a track pass a track configuration object to load_track().  Track configuration
objects are described in theigv.js documentation.Remote URLtrack=IGV.create_track(name="Segmented CN",url="https://data.broadinstitute.org/igvdata/test/igv-web/segmented_data_080520.seg.gz",format="seg",indexed=False)igv.load_track(track)Local FileTracks can be loaded from local files using the Jupyter web server by prepending "tree" to the path.track=IGV.create_track(name="Local VCF",url="/tree/absolute/path/to/example.vcf",format="vcf",type="variant",indexed=False)igv.load_track(track)Remove a track# It is easy to remove a track by nameigv.remove_track("HG00103")NavigationZoom in by a factor of 2igv.zoom_in()Zoom out by a factor of 2igv.zoom_out()Jump to a specific locusigv.locus='chr1:3000-4000'# A helper method is available to avoid having to perform string formattingigv.search_locus('chr1',3000,4000)Jump to a specific gene. This uses the IGV search web service, which currently supports a limited number of genomes:  hg38, hg19, and mm10.
To configure a custom search service see theigv.js documentationigv.locus='myc'SVG outputDisplaying the current IGV view as an SVG is simple - and only requires one call now!igv.get_svg()Development InstallationCreate a dev environment:condacreate-nigv_jupyterlab-dev-cconda-forgenodejsyarnpythonjupyterlab
condaactivateigv_jupyterlab-devInstall the python. This will also build the TS package.pipinstall-e".[test, examples]"When developing your extensions, you need to manually enable your extensions with the
notebook / lab frontend. For lab, this is done by the command:jupyter labextension develop --overwrite .
yarn run buildFor classic notebook, you need to run:jupyter nbextension install --sys-prefix --symlink --overwrite --py igv_jupyterlab
jupyter nbextension enable --sys-prefix --py igv_jupyterlabNote that the--symlinkflag doesn't work on Windows, so you will here have to run
theinstallcommand every time that you rebuild your extension. For certain installations
you might also need another flag instead of--sys-prefix, but we won't cover the meaning
of those flags here.How to see your changesTypescript:If you use JupyterLab to develop then you can watch the source directory and run JupyterLab at the same time in different
terminals to watch for changes in the extension's source and automatically rebuild the widget.# Watch the source directory in one terminal, automatically rebuilding when neededyarnrunwatch# Run JupyterLab in another terminaljupyterlabAfter a change wait for the build to finish and then refresh your browser and the changes should take effect.Python:If you make a change to the python code then you will need to restart the notebook kernel to have it take effect.