malariagen_data.af1.Af1.plot_h12_gwss_multi_panel

Af1.plot_h12_gwss_multi_panel(contig: str, cohorts: str | Mapping[str, str], window_size: int | dict[str, int], cohort_size: int | None = None, sample_query: str | None = None, analysis: str = 'default', min_cohort_size: int | None = 15, max_cohort_size: int | None = 50, sample_query_options: dict | None = None, sample_sets: Sequence[str] | str | None = None, random_seed: int = 42, 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', gene_labels: Mapping[str, str] | None = None, gene_labelset: LabelSet | None = None, chunks: int | str | Tuple[int | str, ...] | Callable[[Tuple[int, ...]], int | str | Tuple[int | str, ...]] = 'native', inline_array: bool = True) → Model | None

Plot h12 GWSS data with multiple tracks.

Parameters

contigstr

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

cohortsstr or Mapping[str, str]

Either a string giving the name of a predefined cohort set (e.g., “admin1_month”) or a dict mapping custom cohort labels to sample queries.

window_sizeint or dict[str, int]

The size of windows (number of SNPs) used to calculate statistics within. Can be a single value, in which case the same window size will be used for all cohorts. Can also be a mapping from cohort identifiers to values, in case you need to provide different window sizes for different cohorts.

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.

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.

analysisstr, optional, default: ‘default’

Which haplotype phasing analysis to use. See the phasing_analysis_ids property for available values.

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.

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.

random_seedint, optional, default: 42

Random seed used for reproducible down-sampling.

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.

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.

chunksint or str or tuple of int or str or Callable[[typing.Tuple[int, …]], int or str or tuple of int or str], optional, default: ‘native’

Define how input data being read from zarr should be divided into chunks for a dask computation. If ‘native’, use underlying zarr chunks. If a string specifying a target memory size, e.g., ‘300 MiB’, resize chunks in arrays with more than one dimension to match this size. If ‘auto’, let dask decide chunk size. If ‘ndauto’, let dask decide chunk size but only for arrays with more than one dimension. If ‘ndauto0’, as ‘ndauto’ but only vary the first chunk dimension. If ‘ndauto1’, as ‘ndauto’ but only vary the second chunk dimension. If ‘ndauto01’, as ‘ndauto’ but only vary the first and second chunk dimensions. Also, can be a tuple of integers, or a callable which accepts the native chunks as a single argument and returns a valid dask chunks value.

inline_arraybool, optional, default: True

Passed through to dask from_array().

Returns

Model or None

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