malariagen_data.af1.Af1.plot_snps_track

Af1.plot_snps_track(region: str | Region | Mapping, sample_sets: Sequence[str] | str | None = None, sample_query: str | None = None, site_mask: str = 'default', cohort_size: int | None = None, 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, max_snps: int = 200000, x_range: Range | None = None, show: bool = True, output_backend: Literal['canvas', 'webgl', 'svg'] = 'webgl') → Model | None

Plot SNPs in a given genome region. SNPs are shown as rectangles, with segregating and non-segregating SNPs positioned on different levels, and coloured by site filter.

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.

sample_setssequence of str or str or None, optional

List of sample sets and/or releases. Can also be a single sample set or release.

sample_querystr or None, optional

A pandas query string to be evaluated against the sample metadata, to select samples to be included in the returned data.

site_maskstr, optional, default: ‘default’

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

cohort_sizeint or None, optional

Randomly down-sample to this value if the number of samples in the cohort is greater. Raise an error if the number of samples is less than this value.

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

Plot height in pixels (px).

max_snpsint, optional, default: 200000

Maximum number of SNPs to show.

x_rangeRange or None, optional

X axis range (for linking to other tracks).

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).