malariagen_data.ag3.Ag3.plot_g123_calibration

Ag3.plot_g123_calibration(contig: str, sites: str, site_mask: str = 'default', sample_query: str | None = None, sample_sets: Sequence[str] | str | None = None, min_cohort_size: int | None = 20, max_cohort_size: int | None = 50, window_sizes: Tuple[int, ...] = (100, 200, 500, 1000, 2000, 5000, 10000, 20000), random_seed: int = 42, title: str | bool | None = None, show: bool = True) → Model | None

Plot g123 GWSS calibration data for different window sizes.

Parameters

contigstr

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

sitesstr

Which sites to use: ‘all’ includes all sites that pass site filters; ‘segregating’ includes only segregating sites for the given cohort; or a phasing analysis identifier can be provided to use sites from the haplotype data, which is an approximation to finding segregating sites in the entire Ag3.0 (gambiae complex) or Af1.0 (funestus) cohort.

site_maskstr, optional, default: ‘default’

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

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_setssequence of str or str or None, optional

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

min_cohort_sizeint or None, optional, default: 20

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.

window_sizestuple of int, optional, default: (100, 200, 500, 1000, 2000, 5000, 10000, 20000)

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

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.

showbool, optional, default: True

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

Returns

Model or None

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