ehrapy.plot.scatter

ehrapy.plot.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, title=None, show=None, save=None, ax=None)[source]

Scatter plot along observations or variables axes.

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

Parameters:

  • adata (AnnData) – AnnData object object containing all observations.

  • x (str | None) – x coordinate (MedCat entities currently not supported)

  • y (str | None) – y coordinate (MedCat entities currently not supported)

  • color (str) – Keys for annotations of observations/patients or features, or a hex color specification, e.g., ‘ann1’, ‘#fe57a1’, or [‘ann1’, ‘ann2’] or extracted entities from ehrapy’s MedCat tool.

  • use_raw (bool | None) – Whether to use raw attribute of adata. Defaults to True if .raw is present.

  • layers (str | Collection[str]) – 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']]) – String that denotes a plotting tool that computed coordinates.

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

  • groups (str | Iterable[str]) – Restrict to a few categories in categorical observation annotation. The default is not to restrict to any groups.

  • components (str | Collection[str]) – For instance, [‘1,2’, ‘2,3’]. To plot all available components use components=’all’.

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

  • legend_loc (str) – 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]) – 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]) – 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) – Line width of the legend font outline in pt. Draws a white outline using the path effect withStroke.

  • size (int | float | None) – Point size. If None, is automatically computed as 120000 / n_features. Can be a sequence containing the size for each observation. The order should be the same as in adata.obs.

  • color_map (str | Colormap) – 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, ...]]]]) – 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 (bool | None) – Draw a frame around the scatter plot. Defaults to value set in set_figure_params() (default: True).

  • title (str | None) – Provide title for panels either as string or list of strings, e.g. [‘title1’, ‘title2’, …].

  • show (bool | None) – Whether to display the figure or return axis.

  • save (str | bool | 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 (Axes | None) – A matplotlib axes object. Only works if plotting a single component.

Returns:

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

Example

import ehrapy as ep

adata = ep.dt.mimic_2(encoded=True)
ep.pp.knn_impute(adata)
ep.pp.log_norm(adata, offset=1)
ep.pp.neighbors(adata)
ep.pl.scatter(adata, x="age", y="icu_los_day", color="icu_los_day")
Preview:
../../_images/scatter.png