cellestial.dimensional#

dimensional(data: AnnData, key: str | None = None, *, mapping: FeatureSpec | None = None, dimensions: Literal['umap', 'pca', 'tsne'] = 'umap', use_key: str | None = None, xy: tuple[int, int] | Sequence[int] = (1, 2), size: float = 0.8, variable_keys: Sequence[str] | str | None = None, tooltips: Literal['none'] | Sequence[str] | FeatureSpec | None = None, interactive: bool = False, observations_name: str = 'Barcode', color_low: str = '#e6e6e6', color_mid: str | None = None, color_high: str = '#377eb8', mid_point: Literal['mean', 'median', 'mid'] | float = 'median', axis_type: Literal['axis', 'arrow'] | None = None, arrow_length: float = 0.25, arrow_size: float = 1, arrow_color: str = '#3f3f3f', arrow_angle: float = 10, legend_ondata: bool = False, ondata_size: float = 12, ondata_color: str = '#3f3f3f', ondata_fontface: str = 'bold', ondata_family: str = 'sans', ondata_alpha: float = 1, ondata_weighted: bool = True, **point_kwargs) → PlotSpec#

Dimensionality reduction plot.

Parameters:

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

  • key (str, default None) – The key (cell feature) to color the points by. e.g., ‘leiden’ or ‘louvain’ to color by clusters or gene name for expression.

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

  • dimensions ({'umap', 'pca', 'tsne'}, default 'umap') – The dimensional reduction method to use. e.g., ‘umap’ or ‘pca’ or ‘tsne’.

  • xy (tuple[int, int] | Sequence[int], default (1, 2)) – The x and y axes to use for the plot. e.g., (1, 2) for UMAP1 and UMAP2.

  • use_key (str, default None) – The specific key to use for the desired dimensions. e.g., ‘X_umap_2d’ or ‘X_pca_2d’. Otherwise, the function will decide on the key based on the dimensions.

  • size (float, default 0.8) – The size of the points.

  • variable_keys (str | Sequence[str] | None, default None) – Variable keys to add to the DataFrame. If None, no additional keys are added.

  • 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.

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

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

  • color_low (str, default '#e6e6e6') –

    The color to use for the low end of the color gradient. - 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)’.

    • Applies to continuous (non-categorical) data.

  • color_mid (str, default None) –

    The color to use for the middle part of the color gradient. - 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)’.

    • Applies to continuous (non-categorical) data.

  • color_high (str, default '#377EB8') –

    The color to use for the high end of the color gradient. - 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)’.

    • Applies to continuous (non-categorical) data.

  • mid_point ({'mean', 'median', 'mid'} | float, default 'median') – The midpoint (in data value) of the color gradient. Can be ‘mean’, ‘median’ and ‘mid’ or a number (float or int). - If ‘mean’, the midpoint is the mean of the data. - If ‘median’, the midpoint is the median of the data. - If ‘mid’, the midpoint is the mean of ‘min’ and ‘max’ of the data.

  • axis_type ({'axis', 'arrow'} | None) – Whether to use regular axis or arrows as the axis.

  • arrow_length (float, default 0.25) – Length of the arrow head (px).

  • arrow_size (float, default 1) – Size of the arrow.

  • arrow_color (str, default '#3f3f3f') –

    Color of the arrows. - 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)’.

    • Applies to continuous (non-categorical) data.

  • arrow_angle (float, default 10) – Angle of the arrow head in degrees.

  • legend_ondata (bool, default False) – whether to show legend on data

  • ondata_size (float, default 12) – size of the legend (text) on data.

  • ondata_color (str, default '#3f3f3f') – color of the legend (text) on data

  • ondata_fontface (str, default 'bold') – fontface of the legend (text) on data. https://lets-plot.org/python/pages/aesthetics.html#font-face

  • ondata_family (str, default 'sans') – family of the legend (text) on data. https://lets-plot.org/python/pages/aesthetics.html#font-family

  • ondata_alpha (float, default 1) – alpha (transparency) of the legend on data.

  • ondata_weighted (bool, default True) – whether to use weighted mean for the legend on data. If True, the weighted mean of the group means is used. If False, the arithmetic mean of the group means is used.

  • **point_kwargs – 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

Returns:

PlotSpec – Dimensional reduction plot.

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