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Plotting tools

utilz.plot

Plotting convenience functions

makefig(figorax, **kwargs)

A context manager to handling a figure and optionally saving it. Handles all kwargs to plt.subplots() as well as a save kwarg that should point to a file to auto-saving

Parameters:

Name Type Description Default
figorax str

'fig' or 'ax'

 required

Yields:

Type Description

figure or axis handle

Examples:

>>> x = np.random.randn(10)
>>> with makefig('ax', figsize=(3,3)) as ax:
>>>    ax.plot(x)

>>> with makefig('ax', save='myfig.jpg') as ax:
>>>    ax.plot(x)
>>>    # figure is saved to 'myfig.jpg'
Source code in utilz/plot.py 
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@contextmanager
def makefig(figorax, **kwargs):
    """
    A context manager to handling a figure and optionally saving it.
    Handles all kwargs to plt.subplots() as well as a save kwarg that
    should point to a file to auto-saving

    Args:
        figorax (str): 'fig' or 'ax'


    Yields:
        figure or axis handle

    Examples:
        >>> x = np.random.randn(10)
        >>> with makefig('ax', figsize=(3,3)) as ax:
        >>>    ax.plot(x)

        >>> with makefig('ax', save='myfig.jpg') as ax:
        >>>    ax.plot(x)
        >>>    # figure is saved to 'myfig.jpg'
    """

    save = kwargs.pop("save", None)
    bbox_inches = kwargs.pop("bbox_inches", "tight")

    f, ax = plt.subplots(**kwargs)
    if figorax == "fig":
        yield f
    elif figorax == "ax":
        yield ax
    else:
        raise ValueError("Fist arg to makefig() must be 'fig' or 'ax'")

    if save is not None:
        f.savefig(save, bbox_inches=bbox_inches)

mpinit(figsize=(8, 6), subplots=(1, 1))

Setup matplotlib subplots boilerplate

Parameters:

Name Type Description Default
figsize tuple

Figure size. Defaults to (8, 6).

 (8, 6)
subplots tuple

subplot grid size. Defaults to (1, 1).

 (1, 1)

Returns:

Name Type Description
tuple Figure, Axes

matplotlib figure handle and axes
Source code in utilz/plot.py 
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def mpinit(figsize: tuple = (8, 6), subplots: tuple = (1, 1)):
    """
    Setup matplotlib subplots boilerplate

    Args:
        figsize (tuple, optional): Figure size. Defaults to (8, 6).
        subplots (tuple, optional): subplot grid size. Defaults to (1, 1).

    Returns:
        tuple ((Figure, Axes)): matplotlib figure handle and axes
    """
    if "plt" not in dir():
        import matplotlib.pyplot as plt
    f, ax = plt.subplots(*subplots, figsize=figsize)
    return f, ax

newax(*args, **kwargs)

Short hand for a new axis on a new figure. Usueful for calling multiple plotting routines in a pipe() but wanting separate figures.

Source code in utilz/plot.py 
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def newax(*args, **kwargs):
    """Short hand for a new axis on a new figure. Usueful for calling multiple plotting
    routines in a pipe() but wanting separate figures."""
    return plt.subplots()[1]

savefig(f, name, path=None, raster=True, vector=True, use_subdirs=True, raster_extension='jpg', vector_extension='svg', bbox_inches='tight', overwrite=True, **kwargs)

Quick figure saving function. Saves raster (jpg) and vector (pdf) by default. Can also optionally prevent file-overwriting

Parameters:

Name Type Description Default
f Figure

matplotlib figure handle

 required
path Path

directory to save figure as a Path object. Defaults to

 None
name str

filename without extension

 required
raster bool

whether to save raster file. Defaults to True.

 True
vector bool

whether to save vector file. Defaults to True.

 True
use_subdirs bool

whether to split saving of raster and vector files

 True
raster_extension str

raster file type. Defaults to "jpg".

 'jpg'
bbox_inches str

see bbox_inches in plt.savefig. Defaults to "tight".

 'tight'
overwrite bool

whether to overwrite any existing files. Defaults to True.

 True
Source code in utilz/plot.py 
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@curry
def savefig(
    f: Figure,
    name: str,
    path: Path = None,
    raster: bool = True,
    vector: bool = True,
    use_subdirs: bool = True,
    raster_extension: str = "jpg",
    vector_extension: str = "svg",
    bbox_inches: str = "tight",
    overwrite: bool = True,
    **kwargs,
) -> None:
    """
    Quick figure saving function. Saves raster (jpg) and vector (pdf) by default. Can
    also optionally prevent file-overwriting

    Args:
        f (Figure): matplotlib figure handle
        path (Path, optional): directory to save figure as a Path object. Defaults to
        None which will save in cwd
        name (str): filename without extension
        raster (bool, optional): whether to save raster file. Defaults to True.
        vector (bool, optional): whether to save vector file. Defaults to True.
        use_subdirs (bool, optional): whether to split saving of raster and vector files
        into subdirectories called 'raster' and 'vector'. Defaults to True.
        raster_extension (str, optional): raster file type. Defaults to "jpg".
        bbox_inches (str, optional): see bbox_inches in plt.savefig. Defaults to "tight".
        overwrite (bool, optional): whether to overwrite any existing files. Defaults to True.

    """
    if isinstance(f, Axes):
        f = f.get_figure()
    if path is not None:
        if not isinstance(path, Path):
            raise TypeError("path must be a `pathlib.Path` object")
    else:
        path = Path.cwd()
    if use_subdirs:
        raster_path = path / "raster" / f"{name}.{raster_extension}"
        vector_path = path / "vector" / f"{name}.{vector_extension}"
    else:
        raster_path = path / f"{name}.{raster_extension}"
        vector_path = path / f"{name}.{vector_extension}"
    if not raster_path.parent.exists():
        raster_path.parent.mkdir()
    if not vector_path.parent.exists():
        vector_path.parent.mkdir()
    if vector:
        if (vector_path.exists() and overwrite) or (not vector_path.exists()):
            f.savefig(vector_path, bbox_inches=bbox_inches, **kwargs)
    if raster:
        if (raster_path.exists() and overwrite) or (not raster_path.exists()):
            f.savefig(raster_path, bbox_inches=bbox_inches, **kwargs)

setcontext(data, context='notebook', font_scale=1, rc=None)

Modify a plot context. Just call it once in a pipe at some point prior to any plot commands or functions. Call it with default args to reset. Intended to be used inside a pipe, because pipe's always reset context before they run

Source code in utilz/plot.py 
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@curry
def setcontext(data, context="notebook", font_scale=1, rc=None):
    """Modify a plot context. Just call it once in a pipe at some point prior to any
    plot commands or functions. Call it with default args to reset. Intended to be used
    inside a pipe, because pipe's always reset context before they run"""

    sns.set_context(context=context, font_scale=font_scale, rc=rc)
    return data

stripbarplot(data, pointcolor='black', remove_duplicate_legend=True, xlabel=None, ylabel=None, xticklabels=None, yticklabels=None, xticks=None, yticks=None, xlim=None, ylim=None, *args, **kwargs)

Combines a call to sns.barplot + sns.stripplot. Optionally set some axis level attributes during plot creation. Leaving these attributes None will return the default labels that seaborn sets.

Parameters:

Name Type Description Default
data DataFrame

input data

 required
pointcolor str

color of stripplot points. Defaults to "black".

 'black'
xlabel [type]

x-axis label. Defaults to seaborn's default.

 None
ylabel [type]

Defaults to seaborn's default.

 None
xticklabels [type]

Defaults to seaborn's default.

 None
yticklabels [type]

Defaults to seaborn's default.

 None
xticks [type]

Defaults to seaborn's default.

 None
yticks [type]

Defaults to seaborn's default.

 None
xlim [type]

Defaults to seaborn's default.

 None
ylim [type]

Defaults to seaborn's default.

 None

Returns:

Name Type Description
Axis Axes

plot axis handle
Source code in utilz/plot.py 
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def stripbarplot(
    data,
    pointcolor="black",
    remove_duplicate_legend=True,
    xlabel=None,
    ylabel=None,
    xticklabels=None,
    yticklabels=None,
    xticks=None,
    yticks=None,
    xlim=None,
    ylim=None,
    *args,
    **kwargs,
) -> Axes:
    """
    Combines a call to `sns.barplot` + `sns.stripplot`. Optionally set some axis level attributes during plot creation. Leaving these attributes None will return the default labels that seaborn sets.

    Args:
        data (DataFrame): input data
        pointcolor (str, optional): color of stripplot points. Defaults to "black".
        xlabel ([type], optional): x-axis label. Defaults to seaborn's default.
        ylabel ([type], optional): Defaults to seaborn's default.
        xticklabels ([type], optional):  Defaults to seaborn's default.
        yticklabels ([type], optional):  Defaults to seaborn's default.
        xticks ([type], optional):  Defaults to seaborn's default.
        yticks ([type], optional):  Defaults to seaborn's default.
        xlim ([type], optional):  Defaults to seaborn's default.
        ylim ([type], optional):  Defaults to seaborn's default.

    Returns:
        Axis: plot axis handle
    """
    ax = kwargs.pop("ax", None)
    if ax == "newax":
        ax = newax()
    estimator = kwargs.pop("estimator", np.mean)
    ncol = kwargs.pop("ncol", None)
    loc = kwargs.pop("loc", None)
    legend = kwargs.pop("legend", None)
    alpha = kwargs.pop("alpha", 1)

    ax = sns.barplot(*args, **kwargs, data=data, ax=ax, estimator=estimator)
    # stripplot doesn't have these kwargs
    _ = kwargs.pop("units", None)
    _ = kwargs.pop("n_boot", None)
    if pointcolor == "hue":
        ax = sns.stripplot(*args, **kwargs, data=data, ax=ax, alpha=alpha)
    else:
        _ = kwargs.pop("palette", None)
        ax = sns.stripplot(
            *args, **kwargs, color=pointcolor, data=data, ax=ax, alpha=alpha
        )

    if legend is False:
        _ = ax.get_legend().remove()

    elif remove_duplicate_legend:
        if ax.get_legend() is not None:
            handles, labels = ax.get_legend_handles_labels()
            half = int(len(handles) / 2)
            if ncol is None:
                if loc is None:
                    legend = ax.legend(handles[half:], labels[half:])
                else:
                    legend = ax.legend(handles[half:], labels[half:], loc=loc)

            elif ncol is not None:
                if loc is None:
                    legend = ax.legend(handles[half:], labels[half:], ncol=ncol)
                else:
                    legend = ax.legend(
                        handles[half:], labels[half:], ncol=ncol, loc=loc
                    )

    if xlabel is not None:
        ax.set_xlabel(xlabel)
    if ylabel is not None:
        ax.set_ylabel(ylabel)
    if xticklabels is not None:
        ax.set_xticklabels(xticklabels)
    if yticklabels is not None:
        ax.set_yticklabels(yticklabels)
    if xticks is not None:
        ax.set_xticks(xticks)
    if yticks is not None:
        ax.set_yticks(yticks)
    if xlim is not None:
        ax.set(xlim=xlim)
    if ylim is not None:
        ax.set(ylim=ylim)
    return ax

tweak(plot, **kwargs)

swiss-army knife to quickly change most aesthetics on a plot, e.g. tick labels, fontsize, etc, in a unified function call

Source code in utilz/plot.py 
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@curry
def tweak(plot: Union[Figure, Axes], **kwargs) -> Union[Figure, Axes]:
    """
    swiss-army knife to quickly change most aesthetics on a plot, e.g. tick labels,
    fontsize, etc, in a unified function call
    """

    # Params that can't be set with ax.set()
    xtick_rotation = kwargs.pop("xtick_rotation", None)
    ytick_rotation = kwargs.pop("ytick_rotation", None)
    xlabel_fontsize = kwargs.pop("xlabel_fontsize", None)
    ylabel_fontsize = kwargs.pop("ylabel_fontsize", None)
    xticklabel_fontsize = kwargs.pop("xticklabel_fontsize", None)
    yticklabel_fontsize = kwargs.pop("yticklabel_fontsize", None)
    despine = kwargs.pop("despine", False)
    tight_layout = kwargs.pop("tight_layout", False)
    handles, labels = plot.get_legend_handles_labels()

    # Title settings
    title = kwargs.get("title", None)
    title_x = kwargs.pop("title_x", None)
    title_y = kwargs.pop("title_y", None)
    title_loc = kwargs.pop("title_loc", None)
    title_fontsize = kwargs.pop("title_fontsize", None)
    title_params = dict(label=title)
    if title_x is not None:
        title_params["x"] = title_x
    if title_y is not None:
        title_params["y"] = title_y
    if title_loc is not None:
        title_params["loc"] = title_loc
    if title_fontsize is not None:
        title_params["fontsize"] = title_fontsize

    # Legend settings
    legend_params = dict()
    legend_params["loc"] = kwargs.pop("loc", "best")
    legend_params["ncols"] = kwargs.pop("ncols", 1)
    legend_params["fontsize"] = kwargs.pop("fontsize", None)
    legend_params["title"] = kwargs.pop("legend_title", None)
    legend_params["title_fontsize"] = kwargs.pop("legend_title_fontsize", None)
    legend_params["fontsize"] = kwargs.pop("legend_labels_fontsize", None)
    legend_params["frameon"] = kwargs.pop("legend_frame", True)
    legend_labels = kwargs.pop("legend_labels", None)
    labels = labels if legend_labels is None else legend_labels

    # Set main params
    plot.set(**kwargs)
    # Set legend params
    if plot.get_legend() is not None:
        plot.legend(handles, labels, **legend_params)
    # Set title params
    plot.set_title(**title_params)
    # Set other params
    if xtick_rotation is not None:
        plot.tick_params(axis="x", rotation=xtick_rotation)
    if ytick_rotation is not None:
        plot.tick_params(axis="y", rotation=ytick_rotation)
    if xlabel_fontsize is not None:
        plot.xaxis.label.set_size(xlabel_fontsize)
    if ylabel_fontsize is not None:
        plot.yaxis.label.set_size(ylabel_fontsize)
    if xticklabel_fontsize is not None:
        plt.tick_params(axis="x", labelsize=xticklabel_fontsize)
    if yticklabel_fontsize is not None:
        plt.tick_params(axis="y", labelsize=yticklabel_fontsize)
    if despine:
        sns.despine(ax=plot)
    if tight_layout:
        plt.tight_layout()

    return plot