Creating components

create(view_type='LGV', **kwargs)

Creates a JBrowseConfig given a view type.

  • create(): creates empty LGV JBrowseConfig

  • create(“CGV”):creates empty CGV JBrowseConfig

  • create(“LGV”, genome=”hg19”):creates LGV JBrowseConfig w/ default genome

  • create(“CGV”, conf={“k”: “v”}):creates CGV JBrowseConfig w/ a conf obj

Parameters
  • view_type (str) – the type of view (‘LGV’ or ‘CGV’), defaults to LGV

  • genome (str) – genome (‘hg19’ or ‘hg38’)

Returns

JBrowseConfig

Return type

JBrowseConfig instance

Raises
  • TypeError – if genome passed is not hg19 or hg38

  • TypeError – if view type is not LGV or CGV

create_component(conf, **kwargs)

Creates a Dash JBrowse LinearGenomeView component given a configuration object and optionally an id.

e.g:

conf = hg38.get_config() create_component(conf,id=”hg38-test”, dash_comp=”CGV”) where hg38 is an instance of JBrowseConfig

Parameters
  • conf (obj) – configuration object from JBrowseConfig instance

  • id (str) – id to use in Dash component

  • dash_comp (str) – (optional) dash component type to create. Currently supporting LGV and CGV. defaults to LGV when no dash_comp= is specified

Returns

Dash JBrowse View given dash_comp type

Return type

Dash JBrowse component

launch(conf, **kwargs)

Launches a LinearGenomeView Dash JBrowse component in a server with the help of JupyterDash.

e.g launch(conf, dash_comp=”CGV”,height=400, port=8002)

Parameters
  • conf (obj) – JBrowseConfiguration object to pass to the Dash JBrowse component

  • id (str) – (optional) id to use for the Dash JBrowse component defaults to jbrowse-component

  • dash_comp (str) – (optional) dash component type to launch. Currently supporting LGV and CGV. defaults to LGV when no dash_comp= is specified

  • port (int) – (optional) port to utilize when running the JupyterDash app

  • height (int) – (optional) the height to utilize for the JupyterDash app