scanpy.pl.scatter

scanpy.pl.scatter(adata, x=None, y=None, color=None, use_raw=None, layers=None, sort_order=True, alpha=None, basis=None, groups=None, components=None, projection='2d', legend_loc='right margin', legend_fontsize=None, legend_fontweight=None, legend_fontoutline=None, color_map=None, palette=None, frameon=None, right_margin=None, left_margin=None, size=None, marker='.', title=None, show=None, save=None, ax=None)

Scatter plot along observations or variables axes.

Color the plot using annotations of observations (.obs), variables (.var) or expression of genes (.var_names).

Parameters:

adata AnnData

Annotated data matrix.

x Optional[str] (default: None)

x coordinate.

y Optional[str] (default: None)

y coordinate.

color str | Collection[str] (default: None)

Keys for annotations of observations/cells or variables/genes, or a hex color specification, e.g., ‘ann1’, ‘#fe57a1’, or [‘ann1’, ‘ann2’].

use_raw Optional[bool] (default: None)

Whether to use raw attribute of adata. Defaults to True if .raw is present.

layers str | Collection[str] (default: None)

Use the layers attribute of adata if present: specify the layer for x, y and color. If layers is a string, then it is expanded to (layers, layers, layers).

basis Optional[Literal['pca', 'tsne', 'umap', 'diffmap', 'draw_graph_fr']] (default: None)

String that denotes a plotting tool that computed coordinates.

sort_order bool (default: True)

For continuous annotations used as color parameter, plot data points with higher values on top of others.

groups str | Iterable[str] (default: None)

Restrict to a few categories in categorical observation annotation. The default is not to restrict to any groups.

dimensions

0-indexed dimensions of the embedding to plot as integers. E.g. [(0, 1), (1, 2)]. Unlike components, this argument is used in the same way as colors, e.g. is used to specify a single plot at a time. Will eventually replace the components argument.

components str | Collection[str] (default: None)

For instance, [‘1,2’, ‘2,3’]. To plot all available components use components=’all’.

projection Literal['2d', '3d'] (default: '2d')

Projection of plot (default: ‘2d’).

legend_loc str (default: 'right margin')

Location of legend, either ‘on data’, ‘right margin’ or a valid keyword for the loc parameter of Legend.

legend_fontsize Union[int, float, Literal['xx-small', 'x-small', 'small', 'medium', 'large', 'x-large', 'xx-large'], None] (default: None)

Numeric size in pt or string describing the size. See set_fontsize().

legend_fontweight Union[int, Literal['light', 'normal', 'medium', 'semibold', 'bold', 'heavy', 'black'], None] (default: None)

Legend font weight. A numeric value in range 0-1000 or a string. Defaults to ‘bold’ if legend_loc == ‘on data’, otherwise to ‘normal’. See set_fontweight().

legend_fontoutline float (default: None)

Line width of the legend font outline in pt. Draws a white outline using the path effect withStroke.

colorbar_loc

Where to place the colorbar for continous variables. If None, no colorbar is added.

size UnionType[int, float, None] (default: None)

Point size. If None, is automatically computed as 120000 / n_cells. Can be a sequence containing the size for each cell. The order should be the same as in adata.obs.

color_map str | Colormap (default: None)

Color map to use for continous variables. Can be a name or a Colormap instance (e.g. “magma”, “viridis” or mpl.cm.cividis), see get_cmap(). If None, the value of mpl.rcParams[“image.cmap”] is used. The default color_map can be set using set_figure_params().

palette Union[Cycler, ListedColormap, str, tuple[float, ...], Sequence[Union[str, tuple[float, ...]]]] (default: None)

Colors to use for plotting categorical annotation groups. The palette can be a valid ListedColormap name (‘Set2’, ‘tab20’, …), a Cycler object, a dict mapping categories to colors, or a sequence of colors. Colors must be valid to matplotlib. (see is_color_like()). If None, mpl.rcParams[“axes.prop_cycle”] is used unless the categorical variable already has colors stored in adata.uns[“{var}_colors”]. If provided, values of adata.uns[“{var}_colors”] will be set.

na_color

Color to use for null or masked values. Can be anything matplotlib accepts as a color. Used for all points if color=None.

na_in_legend

If there are missing values, whether they get an entry in the legend. Currently only implemented for categorical legends.

frameon Optional[bool] (default: None)

Draw a frame around the scatter plot. Defaults to value set in set_figure_params(), defaults to True.

title Optional[str] (default: None)

Provide title for panels either as string or list of strings, e.g. [‘title1’, ‘title2’, …].

show Optional[bool] (default: None)

Show the plot, do not return axis.

save UnionType[str, bool, None] (default: None)

If True or a str, save the figure. A string is appended to the default filename. Infer the filetype if ending on {‘.pdf’, ‘.png’, ‘.svg’}.

ax Optional[Axes] (default: None)

A matplotlib axes object. Only works if plotting a single component.

Returns:

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