mandos.analysis.plots

Complexity

Total Complexity

39

Size/Duplication

Total Lines	339
Duplicated Lines	0 %

Importance

Changes

0

14 Methods

Rating	Name	Duplication	Size	Complexity
A	PlotOptions.width_and_height()	0	3	1
C	_CatPlotter.get_kwargs()	0	29	10
A	ScorePlotter._plot_fold()	0	36	3
A	_HeatPlotter.__post_init__()	0	3	2
A	ProjectionPlotter.plot()	0	22	3
A	MandosPlotter._figure()	0	6	1
A	_RelPlotter.get_kwargs()	0	7	2
A	TauPlotter.plot()	0	20	2
A	HeatmapPlotter.plot()	0	9	2
A	_HeatPlotter.get_kwargs()	0	16	2
A	ScorePlotter._plot_regular()	0	16	1
A	CorrPlotter.plot()	0	31	3
A	MandosPlotter.__post_init__()	0	8	4
A	ScorePlotter.plot()	0	13	3

"""
Plots.
"""
import enum
from collections import Mapping

The name Mapping does not seem to exist in module collections.

from dataclasses import dataclass
from pathlib import Path
from typing import Any, Optional, Tuple, Union

import numpy as np

Unable to import 'numpy'

from typeddfs import TypedDf, AffinityMatrixDf

Unable to import 'typeddfs'

from matplotlib.colors import Colormap

Unable to import 'matplotlib.colors'

from mandos.analysis._plot_utils import MandosPlotStyling, plt, sns, Figure
from mandos.model.utils import CleverEnum
from mandos.analysis.io_defns import (
    PhiPsiSimilarityDfLongForm,
    PsiProjectedDf,
    EnrichmentDf,
    ConcordanceDf,
    SimilarityDfShortForm,
)


EN_DASH = "–"


@enum.unique

Missing class docstring

class RelPlotType(CleverEnum):
    scatter = 1
    line = 2
    regression = 3


@enum.unique

Missing class docstring

class CatPlotType(CleverEnum):
    bar = 1

Black listed name "bar"

    fold = 2
    box = 3
    violin = 4
    strip = 5
    swarm = 6


@dataclass(frozen=True, repr=True)

Missing class docstring

class PlotOptions:
    size: Optional[str]
    stylesheet: Optional[Path]
    rc: Mapping[str, Any]

Attribute name "rc" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

    hue: Optional[str]
    palette: Union[None, Colormap, Mapping[str, str]]
    extra: Mapping[str, Any]

    @property
    def width_and_height(self) -> Tuple[float, float]:

Missing function or method docstring

        return MandosPlotStyling.fig_width_and_height(self.size)


@dataclass(frozen=True, repr=True)

Empty class docstring

class MandosPlotter:
    """"""

    rc: PlotOptions

Attribute name "rc" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

    def __post_init__(self):
        if sns is None or plt is None:
            raise ImportError(
                "Seaborn and matplotlib required for plotting. Install the 'plots' extra."
            )
        bad_kwargs = set(self.__dict__.keys()).intersection(self.rc.extra.keys())
        if len(bad_kwargs) > 0:
            raise ValueError(f"Overlapping args in extra: {bad_kwargs}")

    def _figure(self):
        width, height = self.rc.width_and_height
        fig = plt.gca()
        fig.set_figwidth(width)
        fig.set_figheight(height)
        return fig


@dataclass(frozen=True, repr=True)
class _CatPlotter(MandosPlotter):
    kind: CatPlotType
    group: bool
    ci: float

Attribute name "ci" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

    boot: int
    seed: Optional[int]

    def get_kwargs(

Missing function or method docstring

        self, n_rows: int, n_categories: int, more: Mapping[str, Any]

The argument n_rows seems to be unused.

Wrong hanging indentation before block (add 4 spaces).

    ) -> Mapping[str, Any]:
        kwargs = dict(dropna=False)
        kwargs.update(**more)
        # the aspect probably doesn't matter much, but it definitely shouldn't be 1
        kwargs["aspect"] = n_categories
        if self.kind is CatPlotType.violin:
            kwargs.update(inner="quartile")
        if self.kind in [CatPlotType.bar, CatPlotType.box, CatPlotType.violin]:
            kwargs.update(saturation=1.0)
        if self.kind in [CatPlotType.swarm, CatPlotType.strip]:
            kwargs.update(edgecolor="black")
        if self.kind in [CatPlotType.bar, CatPlotType.fold]:
            kwargs.update(errcolor="black")
        if self.kind in [
            CatPlotType.bar,

Wrong hanging indentation before block (add 4 spaces).

            CatPlotType.fold,

Wrong hanging indentation before block (add 4 spaces).

            CatPlotType.swarm,

Wrong hanging indentation before block (add 4 spaces).

            CatPlotType.strip,

Wrong hanging indentation before block (add 4 spaces).

            CatPlotType.violin,

Wrong hanging indentation before block (add 4 spaces).

        ]:
            kwargs.update(dodge=self.group)
        if self.group and self.kind is CatPlotType.violin and n_categories == 2:
            kwargs.update(dodge=False, split=True)
        if self.rc.extra is not None:
            kwargs.update(**self.rc.extra)
        kwargs.update(seed=self.seed, ci=self.ci, n_boot=self.boot)
        return kwargs


@dataclass(frozen=True, repr=True)
class _RelPlotter(MandosPlotter):
    kind: RelPlotType
    ci: float

Attribute name "ci" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,|_[^\\WA-Z]*|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern)

    boot: int
    seed: Optional[int]

    def get_kwargs(self, n_rows: int, n_cols: int, more: Mapping[str, Any]) -> Mapping[str, Any]:

Missing function or method docstring

The argument n_rows seems to be unused.

The argument n_cols seems to be unused.

        kwargs = dict(dropna=False, dashes=False)
        kwargs.update(**more)
        if self.rc.extra is not None:
            kwargs.update(**self.rc.extra)
        kwargs.update(seed=self.seed, ci=self.ci, n_boot=self.boot)
        return kwargs


@dataclass(frozen=True, repr=True)
class _HeatPlotter(MandosPlotter):
    vmin_percentile: float = 0
    vmax_percentile: float = 100

    def __post_init__(self):
        if self.rc.extra.get("mask") is not None:
            raise ValueError(f"Cannot set mask in {self.__class__.__name__}")

    def get_kwargs(self, data: AffinityMatrixDf, more: Mapping[str, Any]) -> Mapping[str, Any]:

Missing function or method docstring

        vmin = np.quantile(data.flatten(), self.vmin_percentile / 100)
        vmax = np.quantile(data.flatten(), self.vmax_percentile / 100)
        mask = data.values == np.nan
        kwargs = dict(
            vmin=vmin,
            vmax=vmax,
            square=True,
            mask=mask,
            hue=self.rc.hue,
            palette=self.rc.palette,
        )
        if self.rc.extra is not None:
            kwargs.update(**self.rc.extra)
        kwargs.update(**more)
        return kwargs


@dataclass(frozen=True, repr=True)

Empty class docstring

class ScorePlotter(_CatPlotter):
    """"""

    def plot(self, data: EnrichmentDf) -> Figure:

Missing function or method docstring

        data = data.copy()
        data: TypedDf = data
        data.only("score_name")  # make sure
        data[f"object{EN_DASH}predicate"] = data["object"] + " " + data["predicate"]
        data[f"predicate{EN_DASH}object"] = data["predicate"] + " " + data["object"]
        data = data.sort_natural(f"object{EN_DASH}predicate")
        with MandosPlotStyling.context(*self.rc.rc):

Context manager 'generator' doesn't implement __enter__ and __exit__.

            if self.kind is CatPlotType.fold:
                self._plot_fold(data)
            else:
                self._plot_regular(data)
        return self._figure()

    def _plot_fold(self, data: EnrichmentDf):
        kwargs = dict(
            color="black",
            saturation=1,
            errcolor="black",
            dropna=False,
            ci=None,
            hue=self.rc.hue,
            palette=self.rc.palette,
        )
        if self.rc.extra is not None:
            kwargs.update({k: v for k, v in self.rc.extra if k != "saturation"})
        sns.catplot(
            kind="bar",
            x=f"predicate{EN_DASH}object",
            y="background",
            data=data,
            row="key",
            **kwargs,
        )
        kwargs = dict(
            color="black",
            saturation=0.3,
            errcolor="black",
            hue=self.rc.hue,
            palette=self.rc.palette,
        )
        if self.rc.extra is not None:
            kwargs.update(self.rc.extra)
        sns.catplot(
            kind="bar",
            data=data,
            x=f"predicate{EN_DASH}object",
            y="value",
            row="key",
            **kwargs,
        )

    def _plot_regular(self, data: EnrichmentDf):
        keys = data["keys"].unique()
        defaults = dict(
            saturation=1,
            errcolor="black",
            hue=self.rc.hue,
            palette=self.rc.palette,
        )
        kwargs = self.get_kwargs(len(keys), 1, defaults)
        sns.catplot(
            kind=self.kind.name,
            data=data,
            x=f"predicate{EN_DASH}object",
            y="value",
            row="key",
            **kwargs,
        )


@dataclass(frozen=True, repr=True)

Empty class docstring

class TauPlotter(_CatPlotter):
    """ """

    def plot(self, data: ConcordanceDf) -> Figure:

Missing function or method docstring

        phis = data["phi"].unique()
        # psis = data["psi"].unique()
        defaults = dict(
            saturation=1,
            errcolor="black",
            hue=self.rc.hue,
            palette=self.rc.palette,
        )
        kwargs = self.get_kwargs(len(phis), 1, defaults)
        with MandosPlotStyling.context(*self.rc.rc):

Context manager 'generator' doesn't implement __enter__ and __exit__.

            sns.catplot(
                kind=self.kind.name,
                data=data,
                x="psi",
                y="tau",
                row="phi",
                **kwargs,
            )
        return self._figure()


@dataclass(frozen=True, repr=True)

Empty class docstring

class CorrPlotter(_RelPlotter):
    """"""

    def plot(self, data: PhiPsiSimilarityDfLongForm) -> Figure:

Missing function or method docstring

        phis = data["phi"].unique()
        psis = data["psi"].unique()
        with MandosPlotStyling.context(*self.rc.rc):

Context manager 'generator' doesn't implement __enter__ and __exit__.

            if self.kind is RelPlotType.regression:
                defaults = dict(
                    truncate=True,
                    hue=self.rc.hue,
                    palette=self.rc.palette,
                )
                kwargs = self.get_kwargs(len(phis), len(psis), defaults)
                sns.lmplot(
                    data=data,
                    x="phi_value",
                    y="psi_value",
                    row="phi",
                    col="psi",
                    **kwargs,
                )
            else:
                kwargs = self.get_kwargs(len(phis), len(psis), {})
                sns.relplot(
                    kind=self.kind.name,
                    data=data,
                    x="phi_value",
                    y="psi_value",
                    row="phi",
                    col="psi",
                    **kwargs,
                )
        return self._figure()


@dataclass(frozen=True, repr=True)

Missing class docstring

class HeatmapPlotter(_HeatPlotter):
    def plot(self, data: SimilarityDfShortForm) -> Figure:

Missing function or method docstring

        data = data.triangle()
        kwargs = self.get_kwargs(data, {})
        with MandosPlotStyling.context(*self.rc.rc):

Context manager 'generator' doesn't implement __enter__ and __exit__.

            sns.heatmap(
                data,
                **kwargs,
            )
        return self._figure()


@dataclass(frozen=True, repr=True)

Missing class docstring

class ProjectionPlotter(MandosPlotter):
    def plot(self, data: PsiProjectedDf) -> Figure:

Missing function or method docstring

        psis = set(data["psi"].unique())
        width, height = MandosPlotStyling.fig_width_and_height(self.rc.size)
        aspect = width / height
        col_wrap = int(np.ceil(np.sqrt(len(psis)) * aspect))
        kwargs = dict(
            col_wrap=col_wrap,
            hue=self.rc.hue,
            palette=self.rc.palette,
        )
        if self.rc.extra is not None:
            kwargs.update(**self.rc.extra)
        with MandosPlotStyling.context(*self.rc.rc):

Context manager 'generator' doesn't implement __enter__ and __exit__.

            sns.relplot(
                kind="scatter",
                data=data,
                x="x",
                y="y",
                col="psi",
                **kwargs,
            )
        return self._figure()