malariagen_data.ag3.Ag3.plot_heterozygosity

Ag3.plot_heterozygosity(sample: str | int | List[str | int] | Tuple[str | int, ...], region: str | Region | Mapping, window_size: int = 20000, y_max: float = 0.03, circle_kwargs: Mapping | None = None, site_mask: str | None = 'default', sample_set: str | None = None, sizing_mode: Literal['fixed', 'stretch_width', 'stretch_height', 'stretch_both', 'scale_width', 'scale_height', 'scale_both'] = 'stretch_width', width: int | None = None, track_height: int = 170, genes_height: int = 90, show: bool = True, output_backend: Literal['canvas', 'webgl', 'svg'] = 'webgl') → Model | None

Plot windowed heterozygosity for a single sample over a genome region.

Parameters

samplestr or int or list of str or int or tuple of str or int

Sample identifier or index within sample set. Multiple values can also be provided as a list or tuple.

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.

window_sizeint, optional, default: 20000

Number of sites per window.

y_maxfloat, optional, default: 0.03

Y axis limit.

circle_kwargsMapping or None, optional

Passed through to bokeh scatter() function with marker = ‘circle’.

site_maskstr or None, optional, default: ‘default’

Which site filters mask to apply. See the site_mask_ids property for available values.

sample_setstr or None, optional

Sample set identifier.

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).

track_heightint, optional, default: 170

Main track height in pixels (px).

genes_heightint, optional, default: 90

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.

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.

Returns

Model or None

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