malariagen_data.ag3.Ag3.plot_frequencies_heatmap

Ag3.plot_frequencies_heatmap(df: DataFrame, index: str | List[str] | None = 'label', max_len: int | None = 100, col_width: int = 40, row_height: int = 20, x_label: str | None = 'Cohorts', y_label: str | None = 'Variants', colorbar: bool = True, width: int | None = None, height: int | None = None, text_auto: bool | str = '.0%', aspect: Literal['equal', 'auto'] | None = 'auto', color_continuous_scale: str | List[str] | None = 'Reds', title: str | bool | None = True, show: bool = True, renderer: str | None = None, **kwargs) → Figure | None

Plot a heatmap from a pandas DataFrame of frequencies, e.g., output from snp_allele_frequencies() or gene_cnv_frequencies().

Parameters

dfDataFrame

A DataFrame of frequencies, e.g., output from snp_allele_frequencies() or gene_cnv_frequencies().

indexstr or list of str or None, optional, default: ‘label’

One or more column headers that are present in the input dataframe. This becomes the heatmap y-axis row labels. The column/s must produce a unique index.

max_lenint or None, optional, default: 100

Displaying large styled dataframes may cause ipython notebooks to crash. If the input dataframe is larger than this value, an error will be raised.

col_widthint, optional, default: 40

Plot width per column in pixels (px).

row_heightint, optional, default: 20

Plot height per row in pixels (px).

x_labelstr or None, optional, default: ‘Cohorts’

X axis label.

y_labelstr or None, optional, default: ‘Variants’

Y axis label.

colorbarbool, optional, default: True

If False, do not display a color bar.

widthint or None, optional

Figure width in pixels (px).

heightint or None, optional

Figure height in pixels (px).

text_autobool or str, optional, default: ‘.0%’

If True or a string, single-channel img values will be displayed as text. A string like ‘.2f’ will be interpreted as a texttemplate numeric formatting directive.

aspect{‘equal’, ‘auto’} or None, optional, default: ‘auto’

Aspect ratio, see also https://plotly.com/python-api- reference/generated/plotly.express.imshow.

color_continuous_scalestr or list of str or None, optional, default: ‘Reds’

Colormap used to map scalar data to colors (for a 2D image). This parameter is not used for RGB or RGBA images. If a string is provided, it should be the name of a known color scale, and if a list is provided, it should be a list of CSS-compatible colors.

titlestr or bool or None, optional, default: True

If True, attempt to use metadata from input dataset as a plot title. Otherwise, use supplied value as a title.

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.

**kwargs

Passed through to px.imshow().

Returns

Figure or None

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

Notes

It’s recommended to filter the input DataFrame to just rows of interest, i.e., fewer rows than max_len.