malariagen_data.ag3.Ag3.plot_cnv_hmm_coverage

Ag3.plot_cnv_hmm_coverage(sample: str | int | List[str | int] | Tuple[str | int, ...], region: str | Region | Mapping, sample_set: str | None = None, y_max: float | str = 'auto', 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, circle_kwargs: Mapping | None = None, line_kwargs: Mapping | None = None, show: bool = True, output_backend: Literal['canvas', 'webgl', 'svg'] = 'webgl', gene_labels: Mapping[str, str] | None = None, gene_labelset: LabelSet | None = None) → Model | None

Plot CNV HMM data for a single sample, together with a genes track, using bokeh.

Parameters

samplestr or int or list of str or int or tuple of str or int

Sample identifier or index within sample set. Multiple values can also be provided as a list or tuple.

regionstr 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.

sample_setstr or None, optional

Sample set identifier.

y_maxfloat or str, optional, default: ‘auto’

Y axis limit or ‘auto’.

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).

circle_kwargsMapping or None, optional

Passed through to bokeh scatter() function with marker = ‘circle’.

line_kwargsMapping or None, optional

Passed through to bokeh line() function.

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.

Returns

Model or None

Bokeh figure.