malariagen_data.ag3.Ag3.plot_roh

Ag3.plot_roh(sample: str | int, region: str | Region | Mapping, window_size: int = 20000, site_mask: str = 'default', sample_set: str | None = None, phet_roh: float = 0.001, phet_nonroh: Tuple[float, ...] = (0.003, 0.01), transition: float = 0.001, y_max: float = 0.03, sizing_mode: Literal['fixed', 'stretch_width', 'stretch_height', 'stretch_both', 'scale_width', 'scale_height', 'scale_both'] = 'stretch_width', width: int | None = None, heterozygosity_height: int = 170, roh_height: int = 40, genes_height: int = 90, circle_kwargs: Mapping | None = None, show: bool = True, output_backend: Literal['canvas', 'webgl', 'svg'] = 'webgl') → Model | None

Plot windowed heterozygosity and inferred runs of homozygosity for a single sample over a genome region.

Parameters

samplestr or int

Sample identifier or index within sample set.

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.

site_maskstr, 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.

phet_rohfloat, optional, default: 0.001

Probability of observing a heterozygote in a ROH.

phet_nonrohtuple of float, optional, default: (0.003, 0.01)

One or more probabilities of observing a heterozygote outside a ROH.

transitionfloat, optional, default: 0.001

Probability of moving between states. A larger window size may call for a larger transitional probability.

y_maxfloat, optional, default: 0.03

Y axis limit.

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).

heterozygosity_heightint, optional, default: 170

Plot height in pixels (px).

roh_heightint, optional, default: 40

Plot height in pixels (px).

genes_heightint, optional, default: 90

Genes track height in pixels (px).

circle_kwargsMapping or None, optional

Passed through to bokeh circle() function.

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).