malariagen_data.af1.Af1.plot_cnv_hmm_coverage#

Af1.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') 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.

Returns#

Model or None

Bokeh figure.