malariagen_data.ag3.Ag3.plot_aim_heatmap

Ag3.plot_aim_heatmap(aims: str, sample_sets: Sequence[str] | str | None = None, sample_query: str | None = None, sample_query_options: dict | None = None, sort: bool = True, row_height: int = 4, xgap: float = 0, ygap: float = 0.5, palette: Tuple[str, str, str, str] | None = None, show: bool = True, renderer: str | None = None) → Figure | None

Plot a heatmap of ancestry-informative marker (AIM) genotypes.

Parameters

aimsstr

Identifier for a set of ancestry informative markers to use. For possible values see the aim_ids property.

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.

sortbool, optional, default: True

If true (default), sort the samples by the total fraction of AIM alleles for the second species in the comparison.

row_heightint, optional, default: 4

Height per sample in px.

xgapfloat, optional, default: 0

Creates lines between columns (variants).

ygapfloat, optional, default: 0.5

Creates lines between rows (samples).

palettetuple[str, str, str, str] or None, optional

4-tuple of colors for AIM genotypes, in the order: missing, hom taxon 1, het, hom taxon 2.

showbool, optional, default: True

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

rendererstr or None, optional

The name of the renderer to use.

Returns

Figure or None

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