malariagen_data.ag3.Ag3.plot_genes

Ag3.plot_genes(region: str | Region | Mapping, sizing_mode: Literal['fixed', 'stretch_width', 'stretch_height', 'stretch_both', 'scale_width', 'scale_height', 'scale_both'] = 'stretch_width', width: int | None = None, height: int = 120, show: bool = True, toolbar_location: Literal['above', 'below', 'left', 'right'] | None = 'above', x_range: Range | None = None, title: str | bool | None = None, output_backend: Literal['canvas', 'webgl', 'svg'] = 'webgl', gene_labels: Mapping[str, str] | None = None, gene_labelset: LabelSet | None = None) → Model | None

Plot a genes track, using bokeh.

Parameters

regionstr or Region or Mapping

Region of the reference genome. Can be a contig name, region string (formatted like “{contig}:{start}-{end}”), or identifier of a genome feature such as a gene or transcript.

sizing_mode{‘fixed’, ‘stretch_width’, ‘stretch_height’, ‘stretch_both’, ‘scale_width’, ‘scale_height’, ‘scale_both’}, optional, default: ‘stretch_width’

Bokeh plot sizing mode, see also https://docs.bokeh.org/en/latest/docs /user_guide/basic/layouts.html#sizing-modes.

widthint or None, optional

Plot width in pixels (px).

heightint, optional, default: 120

Genes track height in pixels (px).

showbool, optional, default: True

If true, show the plot. If False, do not show the plot, but return the figure.

toolbar_location{‘above’, ‘below’, ‘left’, ‘right’} or None, optional, default: ‘above’

Location of bokeh toolbar.

x_rangeRange or None, optional

X axis range (for linking to other tracks).

titlestr or bool or None, optional

Plot title. If True, a title may be automatically generated.

output_backend{‘canvas’, ‘webgl’, ‘svg’}, optional, default: ‘webgl’

Specify an output backend to render a plot area onto. See also https://docs.bokeh.org/en/latest/docs/user_guide/output/webgl.html.

gene_labelsMapping[str, str] or None, optional

A mapping of gene identifiers to custom labels, which will appear in the plot.

gene_labelsetLabelSet or None, optional

A LabelSet to use in the plot.

Returns

Model or None

A bokeh figure (only returned if show=False).