malariagen_data.af1.Af1.plot_snps

Af1.plot_snps(region: str | Region | Mapping | List[str | Region | Mapping] | Tuple[str | Region | Mapping, ...], sample_sets: Sequence[str] | str | None = None, sample_query: str | None = None, sample_query_options: dict | 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, track_height: int = 80, genes_height: int = 90, max_snps: int = 200000, show: bool = True, gene_labels: Mapping[str, str] | None = None, gene_labelset: LabelSet | None = None) → 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 or list of str or Region or Mapping or tuple of str 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. Can also be a sequence (e.g., list) of regions.

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.

sample_query_optionsdict or None, optional

A dictionary of arguments that will be passed through to pandas query() or eval(), e.g. parser, engine, local_dict, global_dict, resolvers.

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).

track_heightint, optional, default: 80

Plot height in pixels (px).

genes_heightint, optional, default: 90

Genes track height in pixels (px).

max_snpsint, optional, default: 200000

Maximum number of SNPs to show.

showbool, optional, default: True

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

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).