malariagen_data.ag3.Ag3.plot_fst_gwss

Ag3.plot_fst_gwss(contig: str, window_size: int, cohort1_query: str, cohort2_query: str, sample_query_options: dict | None = None, sample_sets: Sequence[str] | str | None = None, site_mask: str | None = 'default', cohort_size: int | None = None, min_cohort_size: int | None = 15, max_cohort_size: int | None = 50, random_seed: int = 42, title: str | bool | 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 = 190, genes_height: int = 90, show: bool = True, output_backend: Literal['canvas', 'webgl', 'svg'] = 'webgl', clip_min: float | None = 0.0, gene_labels: Mapping[str, str] | None = None, gene_labelset: LabelSet | None = None) → Model | None

Run and plot a Fst genome-wide scan to investigate genetic differentiation between two cohorts.

Parameters

contigstr

Reference genome contig name. See the contigs property for valid contig names.

window_sizeint

The size of windows (number of sites) used to calculate statistics within.

cohort1_querystr

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

cohort2_querystr

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.

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.

site_maskstr or None, 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.

min_cohort_sizeint or None, optional, default: 15

Minimum cohort size. Raise an error if the number of samples is less than this value.

max_cohort_sizeint or None, optional, default: 50

Randomly down-sample to this value if the number of samples in the cohort is greater.

random_seedint, optional, default: 42

Random seed used for reproducible down-sampling.

titlestr or bool or None, optional

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

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: 190

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.

clip_minfloat or None, optional, default: 0.0

Minimum value for Fst. Values below this are clipped to this value.

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).