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