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This component can be used as any Dash component in Dash applications. create_component(conf, **kwargs) - creates and returns a Dash JBrowse component -> 'CGV' or 'LGV'.if no genome or conf is passed, you will create an empty JBrowseConfig for that view type.ĭefaults if you pass no params,an empty JBrowse config for a LGV (LinearGenomeView) will be created.Note: you can manually create a conf following the genome: choose from one of our default genomes ).view_type: Choose from a LGV or CGV e.g create('LGV') or create('CGV').
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create(view_type, **kwargs)- creates a JBrowseConfig configuration object given a view_type.The jbrowse-jupyter package provides several utility functions to create and launch Dash JBrowse components in python applications and jupyter notebooks. More information on using a specific environment in Within the myenv conda environment $ pip install jupyterlab Make sure you have jupyter notebook or jupyterlab. To run the Python Dash application $ python browser.py cgv_examples.ipynb - jupyter notebook using the JupyterDash library to embed a Dash JBrowse CircularGenomeView component in a cell.cgv_examples.py - uses the Dash library to create a python application with the Dash JBrowse CircularGenomeView component.browser.ipynb - jupyter notebook using the JupyterDash library to embed a Dash JBrowse LinearGenomeView component in a cell.browser.py - uses the Dash library to create a python application with the Dash JBrowse LinearGenomeView component.You can find examples in the root of this repo, The jbrowse_conf is an instance of our JBrowseConfig, and can be modified to set an assembly, add tracks, set custom color palettes and more.įind more information about the JBrowseConfig API here Other Examples You can customize the Linear Genome View by modifying the jbrowse_conf.
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run_server ( port = 8081, debug = True ) Div (, id = 'test' ) if _name_ = "_main_" : app. get_config () component = create_component ( config ) app. Dash ( _name_ ) jbrowse_conf = create ( "LGV", genome = "hg38" ) config = jbrowse_conf. Launching a Circular Genome View in Jupyter Notebook JBrowse Linear Genome view in python Dash application import dash import dash_html_components as html from jbrowse_jupyter import create, create_component app = dash. Launching a Linear Genome View in Jupyter Notebook Install the JBrowse Jupyter package using pip $ pip install jbrowse-jupyter To create a conda envirnment and install the dependecies. Once you have conda installed, follow the steps found below ipynb filesĬlone this repository and install conda.