From f9b6778877d7f39418aecd4cf3766f8d5ae7f9c1 Mon Sep 17 00:00:00 2001 From: "David H. Hagan" Date: Sun, 21 Apr 2024 20:02:55 -0400 Subject: [PATCH 1/4] Adds regplot --- atmospy/relational.py | 107 +++++++++- poetry.lock | 413 +++++++++++++++++++++------------------ pyproject.toml | 3 +- tests/test_relational.py | 16 ++ 4 files changed, 343 insertions(+), 196 deletions(-) create mode 100644 tests/test_relational.py diff --git a/atmospy/relational.py b/atmospy/relational.py index ecf646b..747c441 100644 --- a/atmospy/relational.py +++ b/atmospy/relational.py @@ -1,14 +1,109 @@ """This file will contain regression figures. """ +import seaborn as sns +import numpy as np +from scipy.stats import ( + linregress, +) from .utils import ( remove_na, -) -from seaborn import ( - FacetGrid, + check_for_numeric_cols ) __all__ = ["regplot", ] -def regplot(): - """Standard regression plot between two variables. - """ \ No newline at end of file +def regplot(data, x, y, fit_reg=True, color=None, marker="o", ylim=None, **kwargs): + """Plot data and a linear regression best fit line between the two variables. + + This function builds on Seaborn's `jointplot` and most kwargs can be passed + straight through to the `jointplot` for customization. + + Parameters + ---------- + data : pd.DataFrame + Input data structure. + x : str + Variable that corresponds to the x data in `data`. + y : str + _description_ + fit_reg : bool, optional + _description_, by default True + color : _type_, optional + _description_, by default None + marker : str, optional + _description_, by default "o" + ylim : _type_, optional + _description_, by default None + """ + check_for_numeric_cols(data, [x, y]) + + # drop NaNs and keep only needed columns + _data = data[[x, y]].dropna(how='any') + + xdata, ydata = _data[x], _data[y] + + # get the range for the plot + if ylim is None: + ymin = min([xdata.min(), ydata.min()]) + ymax = max([xdata.max(), ydata.max()]) + else: + ymin = ylim[0] + ymax = ylim[1] + + if ymax <= ymin: + raise ValueError("`ymax` must be larger than `ymin`") + + # update the kwargs + kwargs.update({"color": color, "marker": marker}) + + # remove certain kwargs that we don't want to allow to be passed to the jointplot + for each in ( + "hue", + "kind", + "dropna", + "xlim", + "ylim", + "hue_order", + "hue_norm" + ): + if each in kwargs: + kwargs.pop(each) + + # set the color if one wasn't explicitly set + if color is None: + color = "C0" + + # make the call to jointplot + g = sns.jointplot( + data=_data, x=x, y=y, kind="scatter", + xlim=(ymin, ymax), + ylim=(ymin, ymax), + **kwargs + ) + + # add a unity line + g.ax_joint.axline( + (0, 0), slope=1, ls='--', + c='k', alpha=0.5, zorder=0, label="1:1" + ) + + # if set, add a regression line + if fit_reg: + _x = np.linspace(ymin, ymax, 10) + res = linregress(xdata, ydata) + + # build the label + label = f"y = {res.slope:.2f}" + if res.intercept < 0: + label += f" - {res.intercept:.2f}" + else: + label += f" + {res.intercept:.2f}" + + # tack on the correlation coef. + label += f"\n$r^2$ = {res.rvalue**2:.3f}" + + g.ax_joint.plot(_x, res.intercept + res.slope*_x, label=label, c=color) + + g.ax_joint.legend() + + return g \ No newline at end of file diff --git a/poetry.lock b/poetry.lock index fc35415..fa6ba38 100644 --- a/poetry.lock +++ b/poetry.lock @@ -719,14 +719,14 @@ files = [ [[package]] name = "exceptiongroup" -version = "1.2.0" +version = "1.2.1" description = "Backport of PEP 654 (exception groups)" category = "dev" optional = false python-versions = ">=3.7" files = [ - {file = "exceptiongroup-1.2.0-py3-none-any.whl", hash = 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analysis and visualization for air quality data." authors = ["David H Hagan "] license = "Apache-2.0" @@ -19,6 +19,7 @@ pandas = ">=1.2" numpy = ">=1.20,<1.24.0 || >1.24.0" matplotlib = ">=3.4,<3.6.1 || >3.6.1" seaborn = ">=0.12" +scipy = ">=1.7" [tool.poetry.dev-dependencies] # pytest = "^6.2.4" diff --git a/tests/test_relational.py b/tests/test_relational.py new file mode 100644 index 0000000..d2e548a --- /dev/null +++ b/tests/test_relational.py @@ -0,0 +1,16 @@ +"""Test the relational plots.""" +import pytest +from atmospy import regplot +import pandas as pd +import matplotlib as mpl +from atmospy import load_dataset +import seaborn as sns + +def test_scatter_basics(): + df = load_dataset("air-sensors-pm") + + ax = regplot( + df, x="Reference", y='Sensor A', + ) + + assert isinstance(ax, sns.axisgrid.JointGrid) \ No newline at end of file From 5675bbe980503fce7415c95a34afdd31da5f14c9 Mon Sep 17 00:00:00 2001 From: "David H. Hagan" Date: Sun, 21 Apr 2024 20:08:38 -0400 Subject: [PATCH 2/4] remove py312 from supported versions for now --- .github/workflows/tests.yml | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 9c34093..a18a83c 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -5,7 +5,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python: ["3.8", "3.9", "3.10", "3.11", "3.12"] + python: ["3.8", "3.9", "3.10", "3.11"] name: Python ${{ matrix.python }} tests steps: - name: Checkout branch diff --git a/pyproject.toml b/pyproject.toml index c2f924a..0ed01f3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -21,7 +21,7 @@ matplotlib = ">=3.4,<3.6.1 || >3.6.1" seaborn = ">=0.12" scipy = ">=1.7" -[tool.poetry.dev-dependencies] +# [tool.poetry.dev-dependencies] # pytest = "^6.2.4" # pytest-cov = "^2.12.1" # jupyter = "^1.0.0" From 59afcc5ca07d7f989ed0bbe09bab94361695ff7a Mon Sep 17 00:00:00 2001 From: "David H. Hagan" Date: Sun, 21 Apr 2024 20:21:26 -0400 Subject: [PATCH 3/4] Updated lock file --- poetry.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/poetry.lock b/poetry.lock index fa6ba38..90e93a8 100644 --- a/poetry.lock +++ b/poetry.lock @@ -3194,4 +3194,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = ">=3.8" -content-hash = "aecb948aab974dc36f216b888b089042c1cb362ce8d58a949bb9a4f7958ef6f8" +content-hash = "da15da61808f17c875a5174626955c40275ae16e78dcde66d4e95202a06ff715" From 579c73d53b97090ab15cac011f806f795acafd45 Mon Sep 17 00:00:00 2001 From: "David H. Hagan" Date: Sun, 21 Apr 2024 21:15:30 -0400 Subject: [PATCH 4/4] Updated gh-actions --- .github/workflows/tests.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index a18a83c..bd61ef4 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -29,10 +29,10 @@ jobs: poetry run pytest tests/ --cov=./ --cov-report=xml - name: Upload coverage to Codecov - uses: codecov/codecov-action@v1 + uses: codecov/codecov-action@v4 with: token: ${{ secrets.CODECOV_TOKEN }} file: ./coverage.xml + slug: dhhagan/atmospy flags: unittests - name: codecov-umbrella - fail_ci_if_error: true \ No newline at end of file + name: codecov-umbrella \ No newline at end of file