data/ehrapy/_utils_doc.py

import inspect
from collections.abc import Callable
from textwrap import dedent


def getdoc(c_or_f: Callable | type) -> str | None:  # pragma: no cover
    if getattr(c_or_f, "__doc__", None) is None:
        return None
    doc = inspect.getdoc(c_or_f)
    if isinstance(c_or_f, type) and hasattr(c_or_f, "__init__"):
        sig = inspect.signature(c_or_f.__init__)  # type: ignore
    else:
        sig = inspect.signature(c_or_f)

    def type_doc(name: str):
        param: inspect.Parameter = sig.parameters[name]
        cls = getattr(param.annotation, "__qualname__", repr(param.annotation))
        if param.default is not param.empty:
            return f"{cls}, optional (default: {param.default!r})"
        else:
            return cls

    return "\n".join(
        f"{line} : {type_doc(line)}" if line.strip() in sig.parameters else line for line in doc.split("\n")
    )


def _doc_params(**kwds):  # pragma: no cover
    """\
    Docstrings should start with "\" in the first line for proper formatting.
    """

    def dec(obj):
        obj.__orig_doc__ = obj.__doc__
        obj.__doc__ = dedent(obj.__doc__).format_map(kwds)
        return obj

    return dec


"""\
Shared docstrings for plotting function parameters.
"""


doc_adata_color_etc = """\
adata: :class:`~anndata.AnnData` object object containing all observations.
        color: Keys for annotations of observations/patients or features, e.g., `'ann1'` or `['ann1', 'ann2']`.
        feature_symbols: Column name in `.var` DataFrame that stores feature symbols. By default `var_names`
                         refer to the index column of the `.var` DataFrame. Setting this option allows alternative names to be used.
        use_raw: Use `.raw` attribute of `adata` for coloring with feature values. If `None`,
                 defaults to `True` if `layer` isn't provided and `adata.raw` is present.
        layer: Name of the AnnData object layer that wants to be plotted. By default
               adata.raw.X is plotted. If `use_raw=False` is set, then `adata.X` is plotted.
               If `layer` is set to a valid layer name, then the layer is plotted. `layer` takes precedence over `use_raw`.\
"""

doc_edges_arrows = """\
edges: Show edges.
        edges_width: Width of edges.
        edges_color: Color of edges. See :func:`~networkx.drawing.nx_pylab.draw_networkx_edges`.
        neighbors_key: Where to look for neighbors connectivities.
                       If not specified, this looks .obsp['connectivities'] for connectivities
                       (default storage place for pp.neighbors). If specified, this looks at
                       `.obsp[.uns[neighbors_key]['connectivities_key']]` for connectivities.
        arrows: Show arrows (deprecated in favour of `scvelo.pl.velocity_embedding`).
        arrows_kwds: Passed to :meth:`~matplotlib.axes.Axes.quiver`\
"""

# Docs for pl.scatter
doc_scatter_basic = """\
sort_order: For continuous annotations used as color parameter, plot data points with higher values on top of others.
        groups: Restrict to a few categories in categorical observation annotation.
                The default is not to restrict to any groups.
        components: For instance, `['1,2', '2,3']`. To plot all available components use `components='all'`.
        projection: Projection of plot (default: `'2d'`).
        legend_loc: Location of legend, either `'on data'`, `'right margin'` or a valid keyword for the `loc` parameter of :class:`~matplotlib.legend.Legend`.
        legend_fontsize: Numeric size in pt or string describing the size. See :meth:`~matplotlib.text.Text.set_fontsize`.
        legend_fontweight: 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 :meth:`~matplotlib.text.Text.set_fontweight`.
        legend_fontoutline: Line width of the legend font outline in pt. Draws a white outline using the path effect :class:`~matplotlib.patheffects.withStroke`.
        size: 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: Color map to use for continous variables. Can be a name or a
                   :class:`~matplotlib.colors.Colormap` instance (e.g. `"magma`", `"viridis"`
                   or `mpl.cm.cividis`), see :func:`~matplotlib.cm.get_cmap`.
                   If `None`, the value of `mpl.rcParams["image.cmap"]` is used.
                   The default `color_map` can be set using :func:`~scanpy.set_figure_params`.
        palette: Colors to use for plotting categorical annotation groups.
                 The palette can be a valid :class:`~matplotlib.colors.ListedColormap` name
                 (`'Set2'`, `'tab20'`, …), a :class:`~cycler.Cycler` object, a dict mapping
                 categories to colors, or a sequence of colors. Colors must be valid to
                 matplotlib. (see :func:`~matplotlib.colors.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: Draw a frame around the scatter plot. Defaults to value set in :func:`~scanpy.set_figure_params` (default: True).
        title: Provide title for panels either as string or list of strings, e.g. `['title1', 'title2', ...]`.\
"""

doc_vbound_percentile = """\
        vmin: The value representing the lower limit of the color scale. Values smaller than vmin are plotted
              with the same color as vmin. vmin can be a number, a string, a function or `None`. If
              vmin is a string and has the format `pN`, this is interpreted as a vmin=percentile(N).
              For example vmin='p1.5' is interpreted as the 1.5 percentile. If vmin is function, then
              vmin is interpreted as the return value of the function over the list of values to plot.
              For example to set vmin tp the mean of the values to plot, `def my_vmin(values): return
              np.mean(values)` and then set `vmin=my_vmin`. If vmin is None (default) an automatic
              minimum value is used as defined by matplotlib `scatter` function. When making multiple
              plots, vmin can be a list of values, one for each plot. For example `vmin=[0.1, 'p1', None, my_vmin]`
        vmax: The value representing the upper limit of the color scale. The format is the same as for `vmin`.
        vcenter: The value representing the center of the color scale. Useful for diverging colormaps.
                 The format is the same as for `vmin`.
                 Example: sc.pl.umap(adata, color='TREM2', vcenter='p50', cmap='RdBu_r')\
"""

doc_vboundnorm = """\
        vmin: The value representing the lower limit of the color scale. Values smaller than vmin are plotted with the same color as vmin.
        vmax: The value representing the upper limit of the color scale. Values larger than vmax are plotted with the same color as vmax.
        vcenter: The value representing the center of the color scale. Useful for diverging colormaps.
        norm: Custom color normalization object from matplotlib. See `https://matplotlib.org/stable/tutorials/colors/colormapnorms.html` for details.\
"""

doc_outline = """\
        add_outline: If set to True, this will add a thin border around groups of dots. In some situations
                     this can enhance the aesthetics of the resulting image
        outline_color: Tuple with two valid color names used to adjust the add_outline. The first color is the
                       border color (default: black), while the second color is a gap color between the
                       border color and the scatter dot (default: white).
        outline_width: Tuple with two width numbers used to adjust the outline. The first value is the width
                       of the border color as a fraction of the scatter dot size (default: 0.3). The second value is
                       width of the gap color (default: 0.05).\
"""

doc_panels = """\
        ncols: Number of panels per row.
               wspace: Adjust the width of the space between multiple panels.
               hspace: Adjust the height of the space between multiple panels.
               return_fig: Return the matplotlib figure.\
"""

# Docs for pl.pca, pl.tsne, … (everything in _tools.scatterplots)
doc_scatter_embedding = f"""\
{doc_scatter_basic}
{doc_vbound_percentile}
{doc_outline}
{doc_panels}
        kwargs: Arguments to pass to :func:`matplotlib.pyplot.scatter`,
                for instance: the maximum and minimum values (e.g. `vmin=-2, vmax=5`).\
"""


doc_show_save_ax = """\
show: Whether to display the figure or return axis.
        save: 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: A matplotlib axes object. Only works if plotting a single component.\
"""

doc_common_plot_args = """\
adata: Annotated data matrix.
        var_names: `var_names` should be a valid subset of `adata.var_names`.
                   If `var_names` is a mapping, then the key is used as label
                   to group the values (see `var_group_labels`). The mapping values
                   should be sequences of valid `adata.var_names`. In this
                   case either coloring or 'brackets' are used for the grouping
                   of var names depending on the plot. When `var_names` is a mapping,
                   then the `var_group_labels` and `var_group_positions` are set.
        groupby: The key of the observation grouping to consider.
        use_raw: Use `raw` attribute of `adata` if present.
        log: Plot on logarithmic axis.
        num_categories: Only used if groupby observation is not categorical. This value
                        determines the number of groups into which the groupby observation should be subdivided.
        categories_order: Order in which to show the categories. Note: add_dendrogram or add_totals
                          can change the categories order.
        figsize: Figure size when `multi_panel=True`. Otherwise the `rcParam['figure.figsize]` value is used.
                 Format is (width, height)
        dendrogram: If True or a valid dendrogram key, a dendrogram based on the hierarchical
                    clustering between the `groupby` categories is added.
                    The dendrogram information is computed using :func:`scanpy.tl.dendrogram`.
                    If `tl.dendrogram` has not been called previously the function is called with default parameters.
        feature_symbols: Column name in `.var` DataFrame that stores feature symbols.
                         By default `var_names` refer to the index column of the `.var` DataFrame.
                         Setting this option allows alternative names to be used.
        var_group_positions: Use this parameter to highlight groups of `var_names`.
                             This will draw a 'bracket' or a color block between the given start and end
                             positions. If the parameter `var_group_labels` is set, the corresponding
                             labels are added on top/left. E.g. `var_group_positions=[(4,10)]`
                             will add a bracket between the fourth `var_name` and the tenth `var_name`.
                             By giving more positions, more brackets/color blocks are drawn.
        var_group_labels: Labels for each of the `var_group_positions` that want to be highlighted.
        var_group_rotation: Label rotation degrees. By default, labels larger than 4 characters are rotated 90 degrees.
        layer: Name of the AnnData object layer that wants to be plotted. By default adata.raw.X is plotted.
               If `use_raw=False` is set, then `adata.X` is plotted. If `layer` is set to a valid layer name,
               then the layer is plotted. `layer` takes precedence over `use_raw`.\
"""

doc_scatter_spatial = """\
library_id: library_id for Visium data, e.g. key in `adata.uns["spatial"]`.
        img_key: Key for image data, used to get `img` and `scale_factor` from `"images"`
                 and `"scalefactors"` entires for this library. To use spatial coordinates,
                 but not plot an image, pass `img_key=None`.
        img: image data to plot, overrides `img_key`.
        scale_factor: Scaling factor used to map from coordinate space to pixel space.
                      Found by default if `library_id` and `img_key` can be resolved. Otherwise defaults to `1.`.
        spot_size: Diameter of spot (in coordinate space) for each point. Diameter
                   in pixels of the spots will be `size * spot_size * scale_factor`.
                   This argument is required if it cannot be resolved from library info.
        crop_coord: Coordinates to use for cropping the image (left, right, top, bottom).
                    These coordinates are expected to be in pixel space (same as `basis`) and will be transformed by `scale_factor`.
                    If not provided, image is automatically cropped to bounds of `basis`, plus a border.
        alpha_img: Alpha value for image.
        bw: Plot image data in gray scale.\
"""

doc_common_groupby_plot_args = """\
title: Title for the figure
        colorbar_title: Title for the color bar. New line character (\\n) can be used.
        cmap: String denoting matplotlib color map.
        standard_scale: Whether or not to standardize the given dimension between 0 and 1, meaning for
                        each variable or group, subtract the minimum and divide each by its maximum.
        swap_axes: By default, the x axis contains `var_names` (e.g. genes) and the y axis
             the `groupby` categories. By setting `swap_axes` then x are the `groupby` categories and y the `var_names`.
        return_fig: Returns :class:`DotPlot` object. Useful for fine-tuning the plot. Takes precedence over `show=False`.\
"""