cellestial.violins

violins(data: AnnData, keys: Sequence[str], *, mapping: FeatureSpec | None = None, axis: Literal[0, 1] | None = None, color: str | None = None, fill: str | None = None, add_keys: Sequence[str] | str | None = None, tooltips: Literal['none'] | Sequence[str] | FeatureSpec | None = None, geom_fill: str = '#FF00FF', geom_color: str = '#2f2f2f', point_color: str = '#1f1f1f', point_alpha: float = 0.7, point_size: float = 0.5, point_geom: Literal['jitter', 'point', 'sina'] = 'jitter', observations_name: str = 'Barcode', variables_name: str = 'Variable', show_points: bool = True, interactive: bool = False, value_column: str = 'value', variable_column: str = 'variable', share_axis: bool = False, share_ticks: bool = False, layers: Sequence[FeatureSpec | LayerSpec] | FeatureSpec | LayerSpec | None = None, ncol: int | None = None, sharex: str | None = None, sharey: str | None = None, widths: list | None = None, heights: list | None = None, hspace: float | None = None, vspace: float | None = None, fit: bool | None = None, align: bool | None = None, guides: str = 'auto', point_kwargs: dict[str, Any] | None = None, **geom_kwargs) → SupPlotsSpec

Violin Plots.

Parameters:

• data (AnnData) – The AnnData object of the single cell data.

• keys (list[str] | tuple[str] | Sequence[str]) – The keys to get the values (numerical). e.g., [‘total_counts’, ‘pct_counts_in_top_50_genes’] or a list of gene names.

• mapping (FeatureSpec | None, default None) – Additional aesthetic mappings for the plot, the result of aes().

• axis ({0,1} | None, default None) – axis of the data, 0 for observations and 1 for variables.

• color (str | None, default None) – Color aesthetic to split the violin plot (categorical). e,g., ‘cell_type’ or ‘leiden’.

• fill (str | None, default None) – Fill aesthetic to split the violin plot (categorical). e,g., ‘cell_type’ or ‘leiden’.

• add_keys (Sequence[str] | str | None, default None) – Additional keys to include in the dataframe.

• tooltips ({'none'} | Sequence[str] | FeatureSpec | None, default None) – Tooltips to show when hovering over the geom. Accepts Sequence[str] or result of layer_tooltips() for more complex tooltips. Use ‘none’ to disable tooltips.

• geom_fill (str, default '#FF00FF') –

  Fill color for all violins in the violin plot. - Accepts:

  • hex code e.g. ‘#f1f1f1’

  • color name (of a limited set of colors).

  • RGB/RGBA e.g. ‘rgb(0, 0, 255)’, ‘rgba(0, 0, 255, 0.5)’.

• geom_color (str, default '#2f2f2f') –

  Border color for all violins in the violin plot. - Accepts:

  • hex code e.g. ‘#f1f1f1’

  • color name (of a limited set of colors).

  • RGB/RGBA e.g. ‘rgb(0, 0, 255)’, ‘rgba(0, 0, 255, 0.5)’.

• point_color (str, default '#1f1f1f') –

  Color for the points in the violin plot. - Accepts:

  • hex code e.g. ‘#f1f1f1’

  • color name (of a limited set of colors).

  • RGB/RGBA e.g. ‘rgb(0, 0, 255)’, ‘rgba(0, 0, 255, 0.5)’.

• point_alpha (float, default 0.7) – Alpha (transparency) for the points in the violin plot.

• point_size (float, default 0.5) – Size for the points in the violin plot.

• point_geom ({'jitter','point','sina'}, default is 'jitter') – Geom type of the points, default is geom_jitter.

• trim (bool, default False) – Whether to trim the violin plot.

• observations_name (str, default 'Barcode') – The name to give to barcode (or index) column in the dataframe.

• variables_name (str, default 'Gene') – The name to give to variable index column in the dataframe.

• show_points (bool, default True) – Whether to show points.

• interactive (bool, default False) – Whether to make the plot interactive.

• share_ticks (bool, default True) – Whether to share the labels across all plots. If True, only X tick texts on bottom row and Y tick text on left column are shown.

• share_axis (bool, default False) – Whether to share the axis across all plots. If True, only X axis on bottom row and Y axis on left column is shown.

• layers (Sequence[FeatureSpec | LayerSpec] | FeatureSpec | LayerSpec | None, default None) – Additional layers to add to the plot.

• variable_column (str, default 'variable') – The name of the variable column in the dataframe.

• value_column (str, default 'value') – The name of the value column in the dataframe.

• ncol (int, default None) – Number of columns in grid. If not specified, shows plots horizontally, in one row.

• sharex (bool, default None) – Controls sharing of axis limits between subplots in the grid. all/True - share limits between all subplots. none/False - do not share limits between subplots. row - share limits between subplots in the same row. col - share limits between subplots in the same column.

• sharey (bool, default None) – Controls sharing of axis limits between subplots in the grid. all/True - share limits between all subplots. none/False - do not share limits between subplots. row - share limits between subplots in the same row. col - share limits between subplots in the same column.

• widths (list[float], default None) – Relative width of each column of grid, left to right.

• heights (list[float], default None) – Relative height of each row of grid, top-down.

• hspace (float | None = None) – Cell horizontal spacing in px.

• vspace (float | None = None) – Cell vertical spacing in px.

• fit (bool, default True) – Whether to stretch each plot to match the aspect ratio of its cell (fit=True), or to preserve the original aspect ratio of plots (fit=False).

• align (bool, default False) – If True, align inner areas (i.e. “geom” bounds) of plots. However, cells containing other (sub)grids are not participating in the plot “inner areas” layouting.

• guides (str, default 'auto') –

  Specifies how guides (legends and colorbars) should be treated in the layout.

  • ’collect’ collect guides from all subplots, removing duplicates.

  • ’keep’ keep guides in their original subplots; do not collect at this level.

  • ’auto’ allow guides to be collected if an upper-level layout uses guides=’collect’;

  otherwise, keep them in subplots. Duplicates are identified by comparing visual properties: For legends: title, labels, and all aesthetic values (colors, shapes, sizes, etc.). For colorbars: title, domain limits, breaks, and color gradient.

  For more information on gggrid parameters: https://lets-plot.org/python/pages/api/lets_plot.gggrid.html

• point_kwargs (dict[str, Any] | None, default None) – Additional parameters for the geom_point layer. For more information on geom_point parameters, see: https://lets-plot.org/python/pages/api/lets_plot.geom_point.html

• **geom_kwargs – Additional parameters for the geom_violin layer. For more information on geom_violin parameters, see: https://lets-plot.org/python/pages/api/lets_plot.geom_violin.html

Returns:

SupPlotsSpec – Violin Plots.