cellfish.plot.embedding

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cellfish.plot.embedding#

cellfish.plot.embedding(adata, basis, *, color=None, gene_symbols=None, use_raw=None, sort_order=True, edges=False, edges_width=0.1, edges_color='grey', neighbors_key=None, arrows=False, arrows_kwds=None, groups=None, components=None, dimensions=None, layer=None, projection='2d', scale_factor=None, color_map=None, cmap=None, palette=None, na_color='lightgray', na_in_legend=True, size=None, axis_type='arrow', colorbar_type='compact', frameon=<object object>, legend_fontsize=None, legend_fontweight='bold', legend_loc='right margin', legend_fontoutline=None, colorbar_loc='right', colorbar_width=None, colorbar_pad=None, colorbar_height_fraction=0.3, vmax=None, vmin=None, vcenter=None, norm=None, add_outline=False, outline_width=(0.3, 0.05), outline_color=('black', 'white'), ncols=4, hspace=0.25, wspace=None, title=None, show=None, save=None, ax=None, return_fig=None, marker='.', **kwargs)#

Scatter plot for user specified embedding basis (e.g. umap, pca, etc).

Parameters:

  • adata (AnnData) – Annotated data matrix.

  • basis (str) – Name of the obsm basis to use.

  • color (Union[str, Sequence[str], None] (default: None)) – Keys for annotations of observations/cells or variables/genes. (None)

  • gene_symbols (Optional[str] (default: None)) – Key for field in .var that stores gene symbols. (None)

  • use_raw (Optional[bool] (default: None)) – Use .raw attribute of adata if present. (None)

  • sort_order (bool (default: True)) – For continuous annotations used as color parameter, plot data points with higher values on top of others. (True)

  • edges (bool (default: False)) – Show edges between cells. (False)

  • edges_width (float (default: 0.1)) – Width of edges. (0.1)

  • edges_color (Union[str, Sequence[float], Sequence[str]] (default: 'grey')) – Color of edges. (‘grey’)

  • neighbors_key (Optional[str] (default: None)) – Key to use for neighbors. (None)

  • arrows (bool (default: False)) – Show arrows for velocity. (False)

  • arrows_kwds (Optional[Mapping[str, Any]] (default: None)) – Keyword arguments for arrow plots. (None)

  • groups (Optional[str] (default: None)) – Groups to highlight. (None)

  • components (Union[str, Sequence[str]] (default: None)) – Components to plot. (None)

  • dimensions (Union[Tuple[int, int], Sequence[Tuple[int, int]], None] (default: None)) – Dimensions to plot. (None)

  • layer (Optional[str] (default: None)) – Name of the layer to use for coloring. (None)

  • projection (Literal['2d', '3d'] (default: '2d')) – Type of projection (‘2d’ or ‘3d’). (‘2d’)

  • scale_factor (Optional[float] (default: None)) – Scaling factor for sizes. (None)

  • color_map (Union[Colormap, str, None] (default: None)) – Colormap to use for continuous variables. (None)

  • cmap (Union[Colormap, str, None] (default: None)) – Colormap to use for continuous variables. (None)

  • palette (Union[str, Sequence[str], Cycler, None] (default: None)) – Colors to use for categorical variables. (None)

  • na_color (str | tuple[float, ...] (default: 'lightgray')) – Color to use for NaN values. (‘lightgray’)

  • na_in_legend (bool (default: True)) – Include NaN values in legend. (True)

  • size (Union[float, Sequence[float], None] (default: None)) – Size of the dots. (None)

  • axis_type (Literal['arrow', 'boxed', 'hidden'] (default: 'arrow')) – Axis styling - 'arrow' (corner arrows), 'boxed' (full spines), or 'hidden' (no axes). ('arrow')

  • colorbar_type (Literal['compact', 'standard'] (default: 'compact')) – Continuous colorbar layout - 'compact' or 'standard'. ('compact')

  • frameon (Union[bool, Literal['small'], None] (default: <object object at 0x7693223c7cd0>)) – Deprecated. Use axis_type and colorbar_type instead.

  • legend_fontsize (Union[int, float, Literal['xx-small', 'x-small', 'small', 'medium', 'large', 'x-large', 'xx-large'], None] (default: None)) – Font size for legend. (None)

  • legend_fontweight (Union[int, Literal['light', 'normal', 'medium', 'semibold', 'bold', 'heavy', 'black']] (default: 'bold')) – Font weight for legend. (‘bold’)

  • legend_loc (str (default: 'right margin')) – Location of legend. (‘right margin’)

  • legend_fontoutline (Optional[int] (default: None)) – Outline width for legend text. (None)

  • colorbar_loc (Optional[str] (default: 'right')) – Location of colorbar. (‘right’)

  • colorbar_width (Optional[float] (default: None)) – Colorbar width as a figure fraction when set; auto-scales from panel width when omitted. (None)

  • colorbar_pad (Optional[float] (default: None)) – Gap between panel and colorbar, as a fraction of panel width. (None)

  • colorbar_height_fraction (float (default: 0.3)) – Colorbar height as a fraction of panel height. (0.3)

  • vmax (Union[str, float, Callable[[Sequence[float]], float], Sequence[str | float | Callable[[Sequence[float]], float]], None] (default: None)) – Maximum value for colorbar. (None)

  • vmin (Union[str, float, Callable[[Sequence[float]], float], Sequence[str | float | Callable[[Sequence[float]], float]], None] (default: None)) – Minimum value for colorbar. (None)

  • vcenter (Union[str, float, Callable[[Sequence[float]], float], Sequence[str | float | Callable[[Sequence[float]], float]], None] (default: None)) – Center value for colorbar. (None)

  • norm (Union[Normalize, Sequence[Normalize], None] (default: None)) – Normalization for colorbar. (None)

  • add_outline (Optional[bool] (default: False)) – Add outline to points. (False)

  • outline_width (Tuple[float, float] (default: (0.3, 0.05))) – Width of outline. ((0.3, 0.05))

  • outline_color (Tuple[str, str] (default: ('black', 'white'))) – Color of outline. ((‘black’, ‘white’))

  • ncols (int (default: 4)) – Number of columns for subplots. (4)

  • hspace (float (default: 0.25)) – Height spacing between subplots. (0.25)

  • wspace (Optional[float] (default: None)) – Width spacing between subplots. (None)

  • title (Union[str, Sequence[str], None] (default: None)) – Title for the plot. (None)

  • show (Optional[bool] (default: None)) – Show the plot. (None)

  • save (Union[bool, str, None] (default: None)) – Save the plot. (None)

  • ax (Optional[Axes] (default: None)) – Matplotlib axes object. (None)

  • return_fig (Optional[bool] (default: None)) – Return figure object. (None)

  • marker (Union[str, Sequence[str]] (default: '.')) – Marker style. (‘.’)

  • **kwargs – Additional keyword arguments.

Returns:

If show==False a Axes or a list of it.

Return type:

ax

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