From 74bab7c49becc408c181602580434e6079441f2e Mon Sep 17 00:00:00 2001
From: Carl Buchholz <32228189+aGuyLearning@users.noreply.github.com>
Date: Fri, 6 Dec 2024 15:58:18 +0100
Subject: [PATCH 01/19] coxph_forestplot

---
 .../docstring_previews/coxph_forestplot.png   | Bin 0 -> 18530 bytes
 ehrapy/plot/__init__.py                       |   2 +-
 ehrapy/plot/_survival_analysis.py             | 102 ++++++++++++++++++
 .../coxph_forestplot_create_expected.ipynb    |  86 +++++++++++++++
 tests/conftest.py                             |   4 +
 .../_images/coxph_forestplot_expected.png     | Bin 0 -> 17755 bytes
 tests/plot/test_catplot.py                    |  15 ++-
 7 files changed, 206 insertions(+), 3 deletions(-)
 create mode 100644 docs/_static/docstring_previews/coxph_forestplot.png
 create mode 100644 tests/_scripts/coxph_forestplot_create_expected.ipynb
 create mode 100644 tests/plot/_images/coxph_forestplot_expected.png

diff --git a/docs/_static/docstring_previews/coxph_forestplot.png b/docs/_static/docstring_previews/coxph_forestplot.png
new file mode 100644
index 0000000000000000000000000000000000000000..82e72b892d14bad910ff79f1737b80796dc196b5
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diff --git a/ehrapy/plot/__init__.py b/ehrapy/plot/__init__.py
index 5ae52ab1..170b9fe9 100644
--- a/ehrapy/plot/__init__.py
+++ b/ehrapy/plot/__init__.py
@@ -2,6 +2,6 @@
 from ehrapy.plot._colormaps import *  # noqa: F403
 from ehrapy.plot._missingno_pl_api import *  # noqa: F403
 from ehrapy.plot._scanpy_pl_api import *  # noqa: F403
-from ehrapy.plot._survival_analysis import kmf, ols
+from ehrapy.plot._survival_analysis import kmf, ols, coxph_forestplot
 from ehrapy.plot.causal_inference._dowhy import causal_effect
 from ehrapy.plot.feature_ranking._feature_importances import rank_features_supervised
diff --git a/ehrapy/plot/_survival_analysis.py b/ehrapy/plot/_survival_analysis.py
index bf74df85..91d78d81 100644
--- a/ehrapy/plot/_survival_analysis.py
+++ b/ehrapy/plot/_survival_analysis.py
@@ -2,9 +2,13 @@
 
 from typing import TYPE_CHECKING
 
+from lifelines import CoxPHFitter
+from matplotlib import gridspec
 import matplotlib.pyplot as plt
+import matplotlib.ticker as ticker
 import numpy as np
 from numpy import ndarray
+import pandas as pd
 
 from ehrapy.plot import scatter
 
@@ -251,3 +255,101 @@ def kmf(
 
     if not show:
         return ax
+
+
+def coxph_forestplot(coxph: CoxPHFitter, 
+                    labels: list[str] | None = None,
+                    fig_size: tuple = (10, 10),
+                    t_adjuster: float = 0.1,
+                    ecolor: str = 'dimgray',
+                    size: int = 3,
+                    marker: str = 'o',
+                    decimal: int = 2,
+                    text_size: int = 12,
+                    color: str = 'k'):
+    """Plots a forest plot of the Cox Proportional Hazard model.
+    Inspired by the forest plot in the zEpid package in Python. 
+    Link: https://zepid.readthedocs.io/en/latest/Graphics.html#effect-measure-plots
+
+    Args:
+        coxph: Fitted CoxPHFitter object.
+        labels: List of labels for each coefficient, default uses the index of the coxph.summary.
+        fig_size: Width, height in inches.
+        t_adjuster: Adjust the table to the right. 
+        ecolor: Color of the error bars.
+        size: Size of the markers.
+        marker: Marker style.
+        decimal: Number of decimal places to display.
+        text_size: Font size of the text.
+        color: Color of the markers.
+
+    Examples:
+        >>> import ehrapy as ep
+        >>> adata = ep.dt.mimic_2(encoded=False)
+        >>> adata_subset = adata[:, ["mort_day_censored", "censor_flg", "gender_num", "afib_flg", "day_icu_intime_num"]]
+        >>> coxph = ep.tl.coxph(adata_subset, event_col="censor_flg", duration_col="mort_day_censored")
+        >>> ep.pl.coxph_forestplot(coxph)
+
+        .. image:: /_static/docstring_previews/coxph_forestplot.png
+
+    """
+
+    data = coxph.summary
+    auc_col = 'coef'
+
+    if labels is None:
+        labels = data.index
+    tval = []
+    ytick = []
+    for i in range(len(data)):
+        if not np.isnan(data[auc_col][i]):
+            if ((isinstance(data[auc_col][i], float)) & (isinstance(data['coef lower 95%'][i], float)) &
+                    (isinstance(data['coef upper 95%'][i], float))):
+                tval.append([round(data[auc_col][i], decimal), (
+                            '(' + str(round(data['coef lower 95%'][i], decimal)) + ', ' +
+                            str(round(data['coef upper 95%'][i], decimal)) + ')')])
+            else:
+                tval.append([data[auc_col][i], ('(' + str(data['coef lower 95%'][i]) + ', ' + str(data['coef upper 95%'][i]) + ')')])
+            ytick.append(i)
+        else:
+            tval.append([' ', ' '])
+            ytick.append(i)
+
+    maxi = round(((pd.to_numeric(data['coef upper 95%'])).max() + 0.1),2)  # setting x-axis maximum 
+
+    mini = round(((pd.to_numeric(data['coef lower 95%'])).min() - 0.1), 1)  # setting x-axis minimum
+    
+    fig = plt.figure(figsize=fig_size)
+    gspec = gridspec.GridSpec(1, 6)  # sets up grid
+    plot = plt.subplot(gspec[0, 0:4])  # plot of data
+    tabl = plt.subplot(gspec[0, 4:])  # table
+    plot.set_ylim(-1, (len(data)))  # spacing out y-axis properly
+    
+    plot.axvline(1, color='gray', zorder=1)
+    lower_diff = data[auc_col] - data['coef lower 95%']
+    upper_diff = data['coef upper 95%'] - data[auc_col]
+    plot.errorbar(data[auc_col], data.index, xerr=[lower_diff, upper_diff], marker='None', zorder=2, ecolor=ecolor, linewidth=0, elinewidth=1)
+    plot.scatter(data[auc_col], data.index, c=color, s=(size * 25), marker=marker, zorder=3, edgecolors='None')
+    plot.xaxis.set_ticks_position('bottom')
+    plot.yaxis.set_ticks_position('left')
+    plot.get_xaxis().set_major_formatter(ticker.ScalarFormatter())
+    plot.get_xaxis().set_minor_formatter(ticker.NullFormatter())
+    plot.set_yticks(ytick)
+    plot.set_xlim([mini, maxi])
+    plot.set_xticks([mini, 1, maxi])
+    plot.set_xticklabels([mini, 1, maxi])
+    plot.set_yticklabels(labels) 
+    plot.tick_params(axis='y', labelsize=text_size)
+    plot.yaxis.set_ticks_position('none')
+    plot.invert_yaxis()  # invert y-axis to align values properly with table
+    tb = tabl.table(cellText=tval, cellLoc='center', loc='right', colLabels=[auc_col, '95% CI'], bbox=[0, t_adjuster, 1, 1])
+    tabl.axis('off')
+    tb.auto_set_font_size(False)
+    tb.set_fontsize(text_size)
+    for _ , cell in tb.get_celld().items():
+        cell.set_linewidth(0)
+    plot.spines["top"].set_visible(False)
+    plot.spines["right"].set_visible(False)
+    plot.spines["left"].set_visible(False)
+    return fig,  plot
+
diff --git a/tests/_scripts/coxph_forestplot_create_expected.ipynb b/tests/_scripts/coxph_forestplot_create_expected.ipynb
new file mode 100644
index 00000000..bcd174c1
--- /dev/null
+++ b/tests/_scripts/coxph_forestplot_create_expected.ipynb
@@ -0,0 +1,86 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%load_ext autoreload\n",
+    "%autoreload 2"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "\n",
+    "import ehrapy as ep\n",
+    "import matplotlib.pyplot as plt"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "current_notebook_dir = %pwd\n",
+    "_TEST_IMAGE_PATH = f\"{current_notebook_dir}/../plot/_images\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "adata = ep.dt.mimic_2(encoded=False)\n",
+    "adata_subset = adata[:, [\"mort_day_censored\", \"censor_flg\", \"gender_num\", \"afib_flg\", \"day_icu_intime_num\"]]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "genderafib_coxph = ep.tl.cox_ph(adata_subset, duration_col=\"mort_day_censored\", event_col=\"censor_flg\")\n",
+    "\n",
+    "fig, ax = ep.pl.coxph_forestplot(genderafib_coxph, fig_size=(12,3), t_adjuster=0.15, marker=\"o\", size=2, text_size=14)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "fig.savefig(f\"{_TEST_IMAGE_PATH}/coxph_forestplot_expected.png\", dpi=80)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.10"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/tests/conftest.py b/tests/conftest.py
index 0983e7d0..56e1be71 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -28,6 +28,10 @@ def root_dir():
 def rng():
     return np.random.default_rng(seed=42)
 
+@pytest.fixture
+def mimic_2():
+    adata = ep.dt.mimic_2()
+    return adata
 
 @pytest.fixture
 def mimic_2_encoded():
diff --git a/tests/plot/_images/coxph_forestplot_expected.png b/tests/plot/_images/coxph_forestplot_expected.png
new file mode 100644
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HcmV?d00001

diff --git a/tests/plot/test_catplot.py b/tests/plot/test_catplot.py
index 64ffb517..a49ed7eb 100644
--- a/tests/plot/test_catplot.py
+++ b/tests/plot/test_catplot.py
@@ -1,16 +1,27 @@
 from pathlib import Path
 
-from ehrapy.plot import catplot
+import ehrapy as ep
 
 CURRENT_DIR = Path(__file__).parent
 _TEST_IMAGE_PATH = f"{CURRENT_DIR}/_images"
 
 
 def test_catplot_vanilla(adata_mini, check_same_image):
-    fig = catplot(adata_mini, jitter=False)
+    fig = ep.pl.catplot(adata_mini, jitter=False)
 
     check_same_image(
         fig=fig,
         base_path=f"{_TEST_IMAGE_PATH}/catplot_vanilla",
         tol=2e-1,
     )
+
+def test_coxph_forestplot(mimic_2, check_same_image):
+    adata_subset = mimic_2[:, ["mort_day_censored", "censor_flg", "gender_num", "afib_flg", "day_icu_intime_num"]]
+    coxph = ep.tl.cox_ph(adata_subset, duration_col="mort_day_censored", event_col="censor_flg")
+    fig, ax = ep.pl.coxph_forestplot(coxph, fig_size=(12,3), t_adjuster=0.15, marker="o", size=2, text_size=14)
+
+    check_same_image(
+        fig=fig,
+        base_path=f"{_TEST_IMAGE_PATH}/coxph_forestplot",
+        tol=2e-1,
+    )

From 39e4d427118f10aba3ca61cf30900d1a128147d0 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 11 Dec 2024 08:17:30 +0000
Subject: [PATCH 02/19] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .github/pull_request_template.md              |   8 +-
 CODE_OF_CONDUCT.md                            |  28 ++---
 README.md                                     |   8 +-
 docs/contributing.md                          |  18 +--
 docs/index.md                                 |   6 +-
 docs/installation.md                          |   8 +-
 ehrapy/plot/__init__.py                       |   2 +-
 ehrapy/plot/_survival_analysis.py             | 116 +++++++++++-------
 .../coxph_forestplot_create_expected.ipynb    |   6 +-
 tests/conftest.py                             |   2 +
 tests/plot/test_catplot.py                    |   3 +-
 11 files changed, 119 insertions(+), 86 deletions(-)

diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
index 4214c3b8..0bafff61 100644
--- a/.github/pull_request_template.md
+++ b/.github/pull_request_template.md
@@ -4,10 +4,10 @@
 
 <!-- Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs). -->
 
--   [ ] This comment contains a description of changes (with reason)
--   [ ] Referenced issue is linked
--   [ ] If you've fixed a bug or added code that should be tested, add tests!
--   [ ] Documentation in `docs` is updated
+- [ ] This comment contains a description of changes (with reason)
+- [ ] Referenced issue is linked
+- [ ] If you've fixed a bug or added code that should be tested, add tests!
+- [ ] Documentation in `docs` is updated
 
 **Description of changes**
 
diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
index d6209cca..39816a93 100644
--- a/CODE_OF_CONDUCT.md
+++ b/CODE_OF_CONDUCT.md
@@ -14,23 +14,23 @@ religion, or sexual identity and orientation.
 Examples of behavior that contributes to creating a positive environment
 include:
 
--   Using welcoming and inclusive language
--   Being respectful of differing viewpoints and experiences
--   Gracefully accepting constructive criticism
--   Focusing on what is best for the community
--   Showing empathy towards other community members
+- Using welcoming and inclusive language
+- Being respectful of differing viewpoints and experiences
+- Gracefully accepting constructive criticism
+- Focusing on what is best for the community
+- Showing empathy towards other community members
 
 Examples of unacceptable behavior by participants include:
 
--   The use of sexualized language or imagery and unwelcome sexual
-    attention or advances
--   Trolling, insulting/derogatory comments, and personal or political
-    attacks
--   Public or private harassment
--   Publishing others’ private information, such as a physical or
-    electronic address, without explicit permission
--   Other conduct which could reasonably be considered inappropriate in a
-    professional setting
+- The use of sexualized language or imagery and unwelcome sexual
+  attention or advances
+- Trolling, insulting/derogatory comments, and personal or political
+  attacks
+- Public or private harassment
+- Publishing others’ private information, such as a physical or
+  electronic address, without explicit permission
+- Other conduct which could reasonably be considered inappropriate in a
+  professional setting
 
 ## Our Responsibilities
 
diff --git a/README.md b/README.md
index 32e66dec..6c4533b4 100644
--- a/README.md
+++ b/README.md
@@ -16,10 +16,10 @@
 
 ## Features
 
--   Exploratory and targeted analysis of Electronic Health Records
--   Quality control & preprocessing
--   Visualization & Exploration
--   Clustering & trajectory inference
+- Exploratory and targeted analysis of Electronic Health Records
+- Quality control & preprocessing
+- Visualization & Exploration
+- Clustering & trajectory inference
 
 ## Installation
 
diff --git a/docs/contributing.md b/docs/contributing.md
index ce5858eb..0a5b318e 100644
--- a/docs/contributing.md
+++ b/docs/contributing.md
@@ -126,11 +126,11 @@ in the cookiecutter-scverse template.
 
 Please write documentation for new or changed features and use-cases. This project uses [sphinx][] with the following features:
 
--   the [myst][] extension allows to write documentation in markdown/Markedly Structured Text
--   Google-style docstrings
--   Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks))
--   [Sphinx autodoc typehints][], to automatically reference annotated input and output types
--   Citations (like {cite:p}`Virshup_2023`) can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/)
+- the [myst][] extension allows to write documentation in markdown/Markedly Structured Text
+- Google-style docstrings
+- Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks))
+- [Sphinx autodoc typehints][], to automatically reference annotated input and output types
+- Citations (like {cite:p}`Virshup_2023`) can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/)
 
 See the [scanpy developer docs](https://scanpy.readthedocs.io/en/latest/dev/documentation.html) for more information
 on how to write documentation.
@@ -144,10 +144,10 @@ These notebooks come from [pert-tutorials](https://github.com/theislab/ehrapy-tu
 
 #### Hints
 
--   If you refer to objects from other packages, please add an entry to `intersphinx_mapping` in `docs/conf.py`. Only
-    if you do so can sphinx automatically create a link to the external documentation.
--   If building the documentation fails because of a missing link that is outside your control, you can add an entry to
-    the `nitpick_ignore` list in `docs/conf.py`
+- If you refer to objects from other packages, please add an entry to `intersphinx_mapping` in `docs/conf.py`. Only
+  if you do so can sphinx automatically create a link to the external documentation.
+- If building the documentation fails because of a missing link that is outside your control, you can add an entry to
+  the `nitpick_ignore` list in `docs/conf.py`
 
 #### Building the docs locally
 
diff --git a/docs/index.md b/docs/index.md
index 56cc3037..03a0987d 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -61,8 +61,8 @@ medRxiv 2023.12.11.23299816; doi: https://doi.org/10.1101/2023.12.11.23299816 ](
 
 # Indices and tables
 
--   {ref}`genindex`
--   {ref}`modindex`
--   {ref}`search`
+- {ref}`genindex`
+- {ref}`modindex`
+- {ref}`search`
 
 [scanpy genome biology (2018)]: https://doi.org/10.1186/s13059-017-1382-0
diff --git a/docs/installation.md b/docs/installation.md
index ba7010a9..b349394e 100644
--- a/docs/installation.md
+++ b/docs/installation.md
@@ -51,10 +51,10 @@ pip install ehrapy[medcat]
 
 Available language models are
 
--   en_core_web_md (python -m spacy download en_core_web_md)
--   en-core-sci-sm (pip install <https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.4.0/en_core_sci_sm-0.4.0.tar.gz>)
--   en-core-sci-md (pip install <https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.4.0/en_core_sci_md-0.4.0.tar.gz>)
--   en-core-sci-lg (pip install <https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.4.0/en_core_sci_lg-0.4.0.tar.gz>)
+- en_core_web_md (python -m spacy download en_core_web_md)
+- en-core-sci-sm (pip install <https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.4.0/en_core_sci_sm-0.4.0.tar.gz>)
+- en-core-sci-md (pip install <https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.4.0/en_core_sci_md-0.4.0.tar.gz>)
+- en-core-sci-lg (pip install <https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.4.0/en_core_sci_lg-0.4.0.tar.gz>)
 
 [github repo]: https://github.com/theislab/ehrapy
 [pip]: https://pip.pypa.io
diff --git a/ehrapy/plot/__init__.py b/ehrapy/plot/__init__.py
index 70ef2e16..de0b75f7 100644
--- a/ehrapy/plot/__init__.py
+++ b/ehrapy/plot/__init__.py
@@ -2,6 +2,6 @@
 from ehrapy.plot._colormaps import *  # noqa: F403
 from ehrapy.plot._missingno_pl_api import *  # noqa: F403
 from ehrapy.plot._scanpy_pl_api import *  # noqa: F403
-from ehrapy.plot._survival_analysis import kaplan_meier, ols, coxph_forestplot
+from ehrapy.plot._survival_analysis import coxph_forestplot, kaplan_meier, ols
 from ehrapy.plot.causal_inference._dowhy import causal_effect
 from ehrapy.plot.feature_ranking._feature_importances import rank_features_supervised
diff --git a/ehrapy/plot/_survival_analysis.py b/ehrapy/plot/_survival_analysis.py
index e4533477..8b9e10d3 100644
--- a/ehrapy/plot/_survival_analysis.py
+++ b/ehrapy/plot/_survival_analysis.py
@@ -3,13 +3,12 @@
 import warnings
 from typing import TYPE_CHECKING
 
-from lifelines import CoxPHFitter
-from matplotlib import gridspec
 import matplotlib.pyplot as plt
 import matplotlib.ticker as ticker
 import numpy as np
-from numpy import ndarray
 import pandas as pd
+from matplotlib import gridspec
+from numpy import ndarray
 
 from ehrapy.plot import scatter
 
@@ -18,7 +17,7 @@
     from xmlrpc.client import Boolean
 
     from anndata import AnnData
-    from lifelines import KaplanMeierFitter
+    from lifelines import CoxPHFitter, KaplanMeierFitter
     from matplotlib.axes import Axes
     from statsmodels.regression.linear_model import RegressionResults
 
@@ -297,29 +296,32 @@ def kaplan_meier(
 
     if not show:
         return ax
-      
+
     else:
         return None
 
-def coxph_forestplot(coxph: CoxPHFitter, 
-                    labels: list[str] | None = None,
-                    fig_size: tuple = (10, 10),
-                    t_adjuster: float = 0.1,
-                    ecolor: str = 'dimgray',
-                    size: int = 3,
-                    marker: str = 'o',
-                    decimal: int = 2,
-                    text_size: int = 12,
-                    color: str = 'k'):
+
+def coxph_forestplot(
+    coxph: CoxPHFitter,
+    labels: list[str] | None = None,
+    fig_size: tuple = (10, 10),
+    t_adjuster: float = 0.1,
+    ecolor: str = "dimgray",
+    size: int = 3,
+    marker: str = "o",
+    decimal: int = 2,
+    text_size: int = 12,
+    color: str = "k",
+):
     """Plots a forest plot of the Cox Proportional Hazard model.
-    Inspired by the forest plot in the zEpid package in Python. 
+    Inspired by the forest plot in the zEpid package in Python.
     Link: https://zepid.readthedocs.io/en/latest/Graphics.html#effect-measure-plots
 
     Args:
         coxph: Fitted CoxPHFitter object.
         labels: List of labels for each coefficient, default uses the index of the coxph.summary.
         fig_size: Width, height in inches.
-        t_adjuster: Adjust the table to the right. 
+        t_adjuster: Adjust the table to the right.
         ecolor: Color of the error bars.
         size: Size of the markers.
         marker: Marker style.
@@ -339,7 +341,7 @@ def coxph_forestplot(coxph: CoxPHFitter,
     """
 
     data = coxph.summary
-    auc_col = 'coef'
+    auc_col = "coef"
 
     if labels is None:
         labels = data.index
@@ -347,52 +349,80 @@ def coxph_forestplot(coxph: CoxPHFitter,
     ytick = []
     for i in range(len(data)):
         if not np.isnan(data[auc_col][i]):
-            if ((isinstance(data[auc_col][i], float)) & (isinstance(data['coef lower 95%'][i], float)) &
-                    (isinstance(data['coef upper 95%'][i], float))):
-                tval.append([round(data[auc_col][i], decimal), (
-                            '(' + str(round(data['coef lower 95%'][i], decimal)) + ', ' +
-                            str(round(data['coef upper 95%'][i], decimal)) + ')')])
+            if (
+                (isinstance(data[auc_col][i], float))
+                & (isinstance(data["coef lower 95%"][i], float))
+                & (isinstance(data["coef upper 95%"][i], float))
+            ):
+                tval.append(
+                    [
+                        round(data[auc_col][i], decimal),
+                        (
+                            "("
+                            + str(round(data["coef lower 95%"][i], decimal))
+                            + ", "
+                            + str(round(data["coef upper 95%"][i], decimal))
+                            + ")"
+                        ),
+                    ]
+                )
             else:
-                tval.append([data[auc_col][i], ('(' + str(data['coef lower 95%'][i]) + ', ' + str(data['coef upper 95%'][i]) + ')')])
+                tval.append(
+                    [
+                        data[auc_col][i],
+                        ("(" + str(data["coef lower 95%"][i]) + ", " + str(data["coef upper 95%"][i]) + ")"),
+                    ]
+                )
             ytick.append(i)
         else:
-            tval.append([' ', ' '])
+            tval.append([" ", " "])
             ytick.append(i)
 
-    maxi = round(((pd.to_numeric(data['coef upper 95%'])).max() + 0.1),2)  # setting x-axis maximum 
+    maxi = round(((pd.to_numeric(data["coef upper 95%"])).max() + 0.1), 2)  # setting x-axis maximum
+
+    mini = round(((pd.to_numeric(data["coef lower 95%"])).min() - 0.1), 1)  # setting x-axis minimum
 
-    mini = round(((pd.to_numeric(data['coef lower 95%'])).min() - 0.1), 1)  # setting x-axis minimum
-    
     fig = plt.figure(figsize=fig_size)
     gspec = gridspec.GridSpec(1, 6)  # sets up grid
     plot = plt.subplot(gspec[0, 0:4])  # plot of data
     tabl = plt.subplot(gspec[0, 4:])  # table
     plot.set_ylim(-1, (len(data)))  # spacing out y-axis properly
-    
-    plot.axvline(1, color='gray', zorder=1)
-    lower_diff = data[auc_col] - data['coef lower 95%']
-    upper_diff = data['coef upper 95%'] - data[auc_col]
-    plot.errorbar(data[auc_col], data.index, xerr=[lower_diff, upper_diff], marker='None', zorder=2, ecolor=ecolor, linewidth=0, elinewidth=1)
-    plot.scatter(data[auc_col], data.index, c=color, s=(size * 25), marker=marker, zorder=3, edgecolors='None')
-    plot.xaxis.set_ticks_position('bottom')
-    plot.yaxis.set_ticks_position('left')
+
+    plot.axvline(1, color="gray", zorder=1)
+    lower_diff = data[auc_col] - data["coef lower 95%"]
+    upper_diff = data["coef upper 95%"] - data[auc_col]
+    plot.errorbar(
+        data[auc_col],
+        data.index,
+        xerr=[lower_diff, upper_diff],
+        marker="None",
+        zorder=2,
+        ecolor=ecolor,
+        linewidth=0,
+        elinewidth=1,
+    )
+    plot.scatter(data[auc_col], data.index, c=color, s=(size * 25), marker=marker, zorder=3, edgecolors="None")
+    plot.xaxis.set_ticks_position("bottom")
+    plot.yaxis.set_ticks_position("left")
     plot.get_xaxis().set_major_formatter(ticker.ScalarFormatter())
     plot.get_xaxis().set_minor_formatter(ticker.NullFormatter())
     plot.set_yticks(ytick)
     plot.set_xlim([mini, maxi])
     plot.set_xticks([mini, 1, maxi])
     plot.set_xticklabels([mini, 1, maxi])
-    plot.set_yticklabels(labels) 
-    plot.tick_params(axis='y', labelsize=text_size)
-    plot.yaxis.set_ticks_position('none')
+    plot.set_yticklabels(labels)
+    plot.tick_params(axis="y", labelsize=text_size)
+    plot.yaxis.set_ticks_position("none")
     plot.invert_yaxis()  # invert y-axis to align values properly with table
-    tb = tabl.table(cellText=tval, cellLoc='center', loc='right', colLabels=[auc_col, '95% CI'], bbox=[0, t_adjuster, 1, 1])
-    tabl.axis('off')
+    tb = tabl.table(
+        cellText=tval, cellLoc="center", loc="right", colLabels=[auc_col, "95% CI"], bbox=[0, t_adjuster, 1, 1]
+    )
+    tabl.axis("off")
     tb.auto_set_font_size(False)
     tb.set_fontsize(text_size)
-    for _ , cell in tb.get_celld().items():
+    for _, cell in tb.get_celld().items():
         cell.set_linewidth(0)
     plot.spines["top"].set_visible(False)
     plot.spines["right"].set_visible(False)
     plot.spines["left"].set_visible(False)
-    return fig,  plot
+    return fig, plot
diff --git a/tests/_scripts/coxph_forestplot_create_expected.ipynb b/tests/_scripts/coxph_forestplot_create_expected.ipynb
index bcd174c1..36d6dea2 100644
--- a/tests/_scripts/coxph_forestplot_create_expected.ipynb
+++ b/tests/_scripts/coxph_forestplot_create_expected.ipynb
@@ -16,9 +16,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "import matplotlib.pyplot as plt\n",
     "\n",
-    "import ehrapy as ep\n",
-    "import matplotlib.pyplot as plt"
+    "import ehrapy as ep"
    ]
   },
   {
@@ -49,7 +49,7 @@
    "source": [
     "genderafib_coxph = ep.tl.cox_ph(adata_subset, duration_col=\"mort_day_censored\", event_col=\"censor_flg\")\n",
     "\n",
-    "fig, ax = ep.pl.coxph_forestplot(genderafib_coxph, fig_size=(12,3), t_adjuster=0.15, marker=\"o\", size=2, text_size=14)"
+    "fig, ax = ep.pl.coxph_forestplot(genderafib_coxph, fig_size=(12, 3), t_adjuster=0.15, marker=\"o\", size=2, text_size=14)"
    ]
   },
   {
diff --git a/tests/conftest.py b/tests/conftest.py
index 56e1be71..6c42f8a7 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -28,11 +28,13 @@ def root_dir():
 def rng():
     return np.random.default_rng(seed=42)
 
+
 @pytest.fixture
 def mimic_2():
     adata = ep.dt.mimic_2()
     return adata
 
+
 @pytest.fixture
 def mimic_2_encoded():
     adata = ep.dt.mimic_2(encoded=True)
diff --git a/tests/plot/test_catplot.py b/tests/plot/test_catplot.py
index a49ed7eb..986de59f 100644
--- a/tests/plot/test_catplot.py
+++ b/tests/plot/test_catplot.py
@@ -15,10 +15,11 @@ def test_catplot_vanilla(adata_mini, check_same_image):
         tol=2e-1,
     )
 
+
 def test_coxph_forestplot(mimic_2, check_same_image):
     adata_subset = mimic_2[:, ["mort_day_censored", "censor_flg", "gender_num", "afib_flg", "day_icu_intime_num"]]
     coxph = ep.tl.cox_ph(adata_subset, duration_col="mort_day_censored", event_col="censor_flg")
-    fig, ax = ep.pl.coxph_forestplot(coxph, fig_size=(12,3), t_adjuster=0.15, marker="o", size=2, text_size=14)
+    fig, ax = ep.pl.coxph_forestplot(coxph, fig_size=(12, 3), t_adjuster=0.15, marker="o", size=2, text_size=14)
 
     check_same_image(
         fig=fig,

From 225b60675b0bb81b76cffddf7a489c4c2dd98487 Mon Sep 17 00:00:00 2001
From: Carl Buchholz <32228189+aGuyLearning@users.noreply.github.com>
Date: Wed, 11 Dec 2024 09:25:16 +0100
Subject: [PATCH 03/19] changed-notebook

---
 docs/tutorials/notebooks | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/tutorials/notebooks b/docs/tutorials/notebooks
index 99b17e70..ac088bca 160000
--- a/docs/tutorials/notebooks
+++ b/docs/tutorials/notebooks
@@ -1 +1 @@
-Subproject commit 99b17e7039699548a908433fa3ee6b5cbac5e29f
+Subproject commit ac088bcabae5de8516ca9a5aa036b4e3cdf67df6

From 47a5b123e01f177551d458689a34f378874975d3 Mon Sep 17 00:00:00 2001
From: Carl Buchholz <32228189+aGuyLearning@users.noreply.github.com>
Date: Wed, 11 Dec 2024 14:33:09 +0100
Subject: [PATCH 04/19] Update ehrapy/plot/_survival_analysis.py

Co-authored-by: Eljas Roellin <65244425+eroell@users.noreply.github.com>
---
 ehrapy/plot/_survival_analysis.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ehrapy/plot/_survival_analysis.py b/ehrapy/plot/_survival_analysis.py
index 8b9e10d3..63d626e0 100644
--- a/ehrapy/plot/_survival_analysis.py
+++ b/ehrapy/plot/_survival_analysis.py
@@ -314,7 +314,7 @@ def coxph_forestplot(
     color: str = "k",
 ):
     """Plots a forest plot of the Cox Proportional Hazard model.
-    Inspired by the forest plot in the zEpid package in Python.
+    Inspired by `zepid.graphics.EffectMeasurePlot <https://readthedocs.org>`_ (zEpid Package, https://pypi.org/project/zepid/).
     Link: https://zepid.readthedocs.io/en/latest/Graphics.html#effect-measure-plots
 
     Args:

From a32c121497f067eefd1e22a97f94fd4cc59d5991 Mon Sep 17 00:00:00 2001
From: Carl Buchholz <32228189+aGuyLearning@users.noreply.github.com>
Date: Wed, 11 Dec 2024 14:41:42 +0100
Subject: [PATCH 05/19] Update ehrapy/plot/_survival_analysis.py

Co-authored-by: Eljas Roellin <65244425+eroell@users.noreply.github.com>
---
 ehrapy/plot/_survival_analysis.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/ehrapy/plot/_survival_analysis.py b/ehrapy/plot/_survival_analysis.py
index 63d626e0..9541882f 100644
--- a/ehrapy/plot/_survival_analysis.py
+++ b/ehrapy/plot/_survival_analysis.py
@@ -315,7 +315,6 @@ def coxph_forestplot(
 ):
     """Plots a forest plot of the Cox Proportional Hazard model.
     Inspired by `zepid.graphics.EffectMeasurePlot <https://readthedocs.org>`_ (zEpid Package, https://pypi.org/project/zepid/).
-    Link: https://zepid.readthedocs.io/en/latest/Graphics.html#effect-measure-plots
 
     Args:
         coxph: Fitted CoxPHFitter object.

From 0c7cd45b7799a2d0ba671778d9079122112e0908 Mon Sep 17 00:00:00 2001
From: Lukas Heumos <lukas.heumos@posteo.net>
Date: Wed, 11 Dec 2024 15:11:32 +0100
Subject: [PATCH 06/19] Remove useless empty line

---
 ehrapy/plot/_survival_analysis.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/ehrapy/plot/_survival_analysis.py b/ehrapy/plot/_survival_analysis.py
index 9541882f..c6c638b1 100644
--- a/ehrapy/plot/_survival_analysis.py
+++ b/ehrapy/plot/_survival_analysis.py
@@ -338,7 +338,6 @@ def coxph_forestplot(
         .. image:: /_static/docstring_previews/coxph_forestplot.png
 
     """
-
     data = coxph.summary
     auc_col = "coef"
 

From 785a2cf7a08eb6ba9486c35732157dbe26e4a2ba Mon Sep 17 00:00:00 2001
From: Lukas Heumos <lukas.heumos@posteo.net>
Date: Wed, 11 Dec 2024 15:11:50 +0100
Subject: [PATCH 07/19] Remove useless comment

---
 ehrapy/plot/_survival_analysis.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ehrapy/plot/_survival_analysis.py b/ehrapy/plot/_survival_analysis.py
index c6c638b1..9302d119 100644
--- a/ehrapy/plot/_survival_analysis.py
+++ b/ehrapy/plot/_survival_analysis.py
@@ -381,7 +381,7 @@ def coxph_forestplot(
     mini = round(((pd.to_numeric(data["coef lower 95%"])).min() - 0.1), 1)  # setting x-axis minimum
 
     fig = plt.figure(figsize=fig_size)
-    gspec = gridspec.GridSpec(1, 6)  # sets up grid
+    gspec = gridspec.GridSpec(1, 6)
     plot = plt.subplot(gspec[0, 0:4])  # plot of data
     tabl = plt.subplot(gspec[0, 4:])  # table
     plot.set_ylim(-1, (len(data)))  # spacing out y-axis properly

From 75ee4ba7256f5787d3067b17323cd4d0ca072be0 Mon Sep 17 00:00:00 2001
From: eroell <eljas.roellin@ikmail.com>
Date: Wed, 11 Dec 2024 15:37:03 +0100
Subject: [PATCH 08/19] undo again; check rtd build

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 78931dcc..7bc35d29 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -99,7 +99,7 @@ docs = [
     "nbsphinx-link",
     "ipykernel",
     "ipython",
-    "ehrapy[dask,medcat]",
+    "ehrapy[dask]",
 ]
 test = [
     "ehrapy[dask]",

From 541e505c9e7c59624f755a3463ad881897ffe611 Mon Sep 17 00:00:00 2001
From: Carl Buchholz <32228189+aGuyLearning@users.noreply.github.com>
Date: Fri, 13 Dec 2024 09:36:27 +0100
Subject: [PATCH 09/19] renamed function and updated documentation to mention,
 that it is a lifelines object

---
 ehrapy/plot/__init__.py           |  2 +-
 ehrapy/plot/_survival_analysis.py | 19 ++++++++++++-------
 tests/plot/test_catplot.py        |  2 +-
 3 files changed, 14 insertions(+), 9 deletions(-)

diff --git a/ehrapy/plot/__init__.py b/ehrapy/plot/__init__.py
index de0b75f7..4a57b84e 100644
--- a/ehrapy/plot/__init__.py
+++ b/ehrapy/plot/__init__.py
@@ -2,6 +2,6 @@
 from ehrapy.plot._colormaps import *  # noqa: F403
 from ehrapy.plot._missingno_pl_api import *  # noqa: F403
 from ehrapy.plot._scanpy_pl_api import *  # noqa: F403
-from ehrapy.plot._survival_analysis import coxph_forestplot, kaplan_meier, ols
+from ehrapy.plot._survival_analysis import cox_ph_forestplot, kaplan_meier, ols
 from ehrapy.plot.causal_inference._dowhy import causal_effect
 from ehrapy.plot.feature_ranking._feature_importances import rank_features_supervised
diff --git a/ehrapy/plot/_survival_analysis.py b/ehrapy/plot/_survival_analysis.py
index 9302d119..8a05ef6c 100644
--- a/ehrapy/plot/_survival_analysis.py
+++ b/ehrapy/plot/_survival_analysis.py
@@ -301,8 +301,8 @@ def kaplan_meier(
         return None
 
 
-def coxph_forestplot(
-    coxph: CoxPHFitter,
+def cox_ph_forestplot(
+    cox_ph: CoxPHFitter,
     labels: list[str] | None = None,
     fig_size: tuple = (10, 10),
     t_adjuster: float = 0.1,
@@ -313,11 +313,12 @@ def coxph_forestplot(
     text_size: int = 12,
     color: str = "k",
 ):
-    """Plots a forest plot of the Cox Proportional Hazard model.
+    """Generates a forest plot to visualize the coefficients and confidence intervals of a Cox Proportional Hazards model. 
+    The method requires a fitted CoxPHFitter object from the lifelines library.
     Inspired by `zepid.graphics.EffectMeasurePlot <https://readthedocs.org>`_ (zEpid Package, https://pypi.org/project/zepid/).
 
     Args:
-        coxph: Fitted CoxPHFitter object.
+        coxph: Fitted CoxPHFitter object from the lifelines library.
         labels: List of labels for each coefficient, default uses the index of the coxph.summary.
         fig_size: Width, height in inches.
         t_adjuster: Adjust the table to the right.
@@ -332,13 +333,17 @@ def coxph_forestplot(
         >>> import ehrapy as ep
         >>> adata = ep.dt.mimic_2(encoded=False)
         >>> adata_subset = adata[:, ["mort_day_censored", "censor_flg", "gender_num", "afib_flg", "day_icu_intime_num"]]
-        >>> coxph = ep.tl.coxph(adata_subset, event_col="censor_flg", duration_col="mort_day_censored")
-        >>> ep.pl.coxph_forestplot(coxph)
+        >>> coxph = ep.tl.cox_ph(adata_subset, event_col="censor_flg", duration_col="mort_day_censored")
+        >>> ep.pl.cox_ph_forestplot(coxph)
 
         .. image:: /_static/docstring_previews/coxph_forestplot.png
 
     """
-    data = coxph.summary
+    # check that the coxph object is fitted
+    if not cox_ph._fitted:
+        raise ValueError("The CoxPHFitter object must be fitted")
+    
+    data = cox_ph.summary
     auc_col = "coef"
 
     if labels is None:
diff --git a/tests/plot/test_catplot.py b/tests/plot/test_catplot.py
index 986de59f..90b2b5f3 100644
--- a/tests/plot/test_catplot.py
+++ b/tests/plot/test_catplot.py
@@ -19,7 +19,7 @@ def test_catplot_vanilla(adata_mini, check_same_image):
 def test_coxph_forestplot(mimic_2, check_same_image):
     adata_subset = mimic_2[:, ["mort_day_censored", "censor_flg", "gender_num", "afib_flg", "day_icu_intime_num"]]
     coxph = ep.tl.cox_ph(adata_subset, duration_col="mort_day_censored", event_col="censor_flg")
-    fig, ax = ep.pl.coxph_forestplot(coxph, fig_size=(12, 3), t_adjuster=0.15, marker="o", size=2, text_size=14)
+    fig, ax = ep.pl.cox_ph_forestplot(coxph, fig_size=(12, 3), t_adjuster=0.15, marker="o", size=2, text_size=14)
 
     check_same_image(
         fig=fig,

From ca4530ac9167499e1ca5c073be4e9a17cc2c5ebe Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 13 Dec 2024 08:37:46 +0000
Subject: [PATCH 10/19] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 ehrapy/plot/_survival_analysis.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/ehrapy/plot/_survival_analysis.py b/ehrapy/plot/_survival_analysis.py
index 8a05ef6c..6ecc9af4 100644
--- a/ehrapy/plot/_survival_analysis.py
+++ b/ehrapy/plot/_survival_analysis.py
@@ -313,7 +313,7 @@ def cox_ph_forestplot(
     text_size: int = 12,
     color: str = "k",
 ):
-    """Generates a forest plot to visualize the coefficients and confidence intervals of a Cox Proportional Hazards model. 
+    """Generates a forest plot to visualize the coefficients and confidence intervals of a Cox Proportional Hazards model.
     The method requires a fitted CoxPHFitter object from the lifelines library.
     Inspired by `zepid.graphics.EffectMeasurePlot <https://readthedocs.org>`_ (zEpid Package, https://pypi.org/project/zepid/).
 
@@ -342,7 +342,7 @@ def cox_ph_forestplot(
     # check that the coxph object is fitted
     if not cox_ph._fitted:
         raise ValueError("The CoxPHFitter object must be fitted")
-    
+
     data = cox_ph.summary
     auc_col = "coef"
 

From f77f4681e26f87ea76337a5b2a7e45f6af985e6f Mon Sep 17 00:00:00 2001
From: Carl Buchholz <32228189+aGuyLearning@users.noreply.github.com>
Date: Fri, 13 Dec 2024 09:40:52 +0100
Subject: [PATCH 11/19] removed fitted check and updated name in notebook

---
 ehrapy/plot/_survival_analysis.py                     | 4 ----
 tests/_scripts/coxph_forestplot_create_expected.ipynb | 2 +-
 2 files changed, 1 insertion(+), 5 deletions(-)

diff --git a/ehrapy/plot/_survival_analysis.py b/ehrapy/plot/_survival_analysis.py
index 6ecc9af4..ca99ebe5 100644
--- a/ehrapy/plot/_survival_analysis.py
+++ b/ehrapy/plot/_survival_analysis.py
@@ -339,10 +339,6 @@ def cox_ph_forestplot(
         .. image:: /_static/docstring_previews/coxph_forestplot.png
 
     """
-    # check that the coxph object is fitted
-    if not cox_ph._fitted:
-        raise ValueError("The CoxPHFitter object must be fitted")
-
     data = cox_ph.summary
     auc_col = "coef"
 
diff --git a/tests/_scripts/coxph_forestplot_create_expected.ipynb b/tests/_scripts/coxph_forestplot_create_expected.ipynb
index 36d6dea2..d75d8d2d 100644
--- a/tests/_scripts/coxph_forestplot_create_expected.ipynb
+++ b/tests/_scripts/coxph_forestplot_create_expected.ipynb
@@ -49,7 +49,7 @@
    "source": [
     "genderafib_coxph = ep.tl.cox_ph(adata_subset, duration_col=\"mort_day_censored\", event_col=\"censor_flg\")\n",
     "\n",
-    "fig, ax = ep.pl.coxph_forestplot(genderafib_coxph, fig_size=(12, 3), t_adjuster=0.15, marker=\"o\", size=2, text_size=14)"
+    "fig, ax = ep.pl.cox_ph_forestplot(genderafib_coxph, fig_size=(12, 3), t_adjuster=0.15, marker=\"o\", size=2, text_size=14)"
    ]
   },
   {

From 66815c4f0adb17ef1a68feccb9a9b4cc07202c51 Mon Sep 17 00:00:00 2001
From: Carl Buchholz <32228189+aGuyLearning@users.noreply.github.com>
Date: Fri, 13 Dec 2024 09:43:02 +0100
Subject: [PATCH 12/19] Update ehrapy/plot/_survival_analysis.py

Co-authored-by: Lukas Heumos <lukas.heumos@posteo.net>
---
 ehrapy/plot/_survival_analysis.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/ehrapy/plot/_survival_analysis.py b/ehrapy/plot/_survival_analysis.py
index ca99ebe5..285b57ac 100644
--- a/ehrapy/plot/_survival_analysis.py
+++ b/ehrapy/plot/_survival_analysis.py
@@ -315,6 +315,7 @@ def cox_ph_forestplot(
 ):
     """Generates a forest plot to visualize the coefficients and confidence intervals of a Cox Proportional Hazards model.
     The method requires a fitted CoxPHFitter object from the lifelines library.
+
     Inspired by `zepid.graphics.EffectMeasurePlot <https://readthedocs.org>`_ (zEpid Package, https://pypi.org/project/zepid/).
 
     Args:

From 76f0f0cb487fb2790adc9aea1b7a093f608ad775 Mon Sep 17 00:00:00 2001
From: Carl Buchholz <32228189+aGuyLearning@users.noreply.github.com>
Date: Fri, 13 Dec 2024 10:01:03 +0100
Subject: [PATCH 13/19] updated variable names and moved test to better file

---
 ehrapy/plot/_survival_analysis.py    | 46 ++++++++++++++--------------
 tests/plot/test_catplot.py           | 11 -------
 tests/plot/test_survival_analysis.py | 17 ++++++++++
 3 files changed, 40 insertions(+), 34 deletions(-)
 create mode 100644 tests/plot/test_survival_analysis.py

diff --git a/ehrapy/plot/_survival_analysis.py b/ehrapy/plot/_survival_analysis.py
index 285b57ac..6dacc124 100644
--- a/ehrapy/plot/_survival_analysis.py
+++ b/ehrapy/plot/_survival_analysis.py
@@ -340,28 +340,28 @@ def cox_ph_forestplot(
         .. image:: /_static/docstring_previews/coxph_forestplot.png
 
     """
-    data = cox_ph.summary
+    coxph_summary = cox_ph.summary
     auc_col = "coef"
 
     if labels is None:
-        labels = data.index
+        labels = coxph_summary.index
     tval = []
     ytick = []
-    for i in range(len(data)):
-        if not np.isnan(data[auc_col][i]):
+    for i in range(len(coxph_summary)):
+        if not np.isnan(coxph_summary[auc_col][i]):
             if (
-                (isinstance(data[auc_col][i], float))
-                & (isinstance(data["coef lower 95%"][i], float))
-                & (isinstance(data["coef upper 95%"][i], float))
+                (isinstance(coxph_summary[auc_col][i], float))
+                & (isinstance(coxph_summary["coef lower 95%"][i], float))
+                & (isinstance(coxph_summary["coef upper 95%"][i], float))
             ):
                 tval.append(
                     [
-                        round(data[auc_col][i], decimal),
+                        round(coxph_summary[auc_col][i], decimal),
                         (
                             "("
-                            + str(round(data["coef lower 95%"][i], decimal))
+                            + str(round(coxph_summary["coef lower 95%"][i], decimal))
                             + ", "
-                            + str(round(data["coef upper 95%"][i], decimal))
+                            + str(round(coxph_summary["coef upper 95%"][i], decimal))
                             + ")"
                         ),
                     ]
@@ -369,8 +369,8 @@ def cox_ph_forestplot(
             else:
                 tval.append(
                     [
-                        data[auc_col][i],
-                        ("(" + str(data["coef lower 95%"][i]) + ", " + str(data["coef upper 95%"][i]) + ")"),
+                        coxph_summary[auc_col][i],
+                        ("(" + str(coxph_summary["coef lower 95%"][i]) + ", " + str(coxph_summary["coef upper 95%"][i]) + ")"),
                     ]
                 )
             ytick.append(i)
@@ -378,22 +378,22 @@ def cox_ph_forestplot(
             tval.append([" ", " "])
             ytick.append(i)
 
-    maxi = round(((pd.to_numeric(data["coef upper 95%"])).max() + 0.1), 2)  # setting x-axis maximum
+    x_axis_upper_bound = round(((pd.to_numeric(coxph_summary["coef upper 95%"])).max() + 0.1), 2)
 
-    mini = round(((pd.to_numeric(data["coef lower 95%"])).min() - 0.1), 1)  # setting x-axis minimum
+    x_axis_lower_bound = round(((pd.to_numeric(coxph_summary["coef lower 95%"])).min() - 0.1), 1)
 
     fig = plt.figure(figsize=fig_size)
     gspec = gridspec.GridSpec(1, 6)
     plot = plt.subplot(gspec[0, 0:4])  # plot of data
     tabl = plt.subplot(gspec[0, 4:])  # table
-    plot.set_ylim(-1, (len(data)))  # spacing out y-axis properly
+    plot.set_ylim(-1, (len(coxph_summary)))  # spacing out y-axis properly
 
     plot.axvline(1, color="gray", zorder=1)
-    lower_diff = data[auc_col] - data["coef lower 95%"]
-    upper_diff = data["coef upper 95%"] - data[auc_col]
+    lower_diff = coxph_summary[auc_col] - coxph_summary["coef lower 95%"]
+    upper_diff = coxph_summary["coef upper 95%"] - coxph_summary[auc_col]
     plot.errorbar(
-        data[auc_col],
-        data.index,
+        coxph_summary[auc_col],
+        coxph_summary.index,
         xerr=[lower_diff, upper_diff],
         marker="None",
         zorder=2,
@@ -401,15 +401,15 @@ def cox_ph_forestplot(
         linewidth=0,
         elinewidth=1,
     )
-    plot.scatter(data[auc_col], data.index, c=color, s=(size * 25), marker=marker, zorder=3, edgecolors="None")
+    plot.scatter(coxph_summary[auc_col], coxph_summary.index, c=color, s=(size * 25), marker=marker, zorder=3, edgecolors="None")
     plot.xaxis.set_ticks_position("bottom")
     plot.yaxis.set_ticks_position("left")
     plot.get_xaxis().set_major_formatter(ticker.ScalarFormatter())
     plot.get_xaxis().set_minor_formatter(ticker.NullFormatter())
     plot.set_yticks(ytick)
-    plot.set_xlim([mini, maxi])
-    plot.set_xticks([mini, 1, maxi])
-    plot.set_xticklabels([mini, 1, maxi])
+    plot.set_xlim([x_axis_lower_bound, x_axis_upper_bound])
+    plot.set_xticks([x_axis_lower_bound, 1, x_axis_upper_bound])
+    plot.set_xticklabels([x_axis_lower_bound, 1, x_axis_upper_bound])
     plot.set_yticklabels(labels)
     plot.tick_params(axis="y", labelsize=text_size)
     plot.yaxis.set_ticks_position("none")
diff --git a/tests/plot/test_catplot.py b/tests/plot/test_catplot.py
index 90b2b5f3..8e569928 100644
--- a/tests/plot/test_catplot.py
+++ b/tests/plot/test_catplot.py
@@ -15,14 +15,3 @@ def test_catplot_vanilla(adata_mini, check_same_image):
         tol=2e-1,
     )
 
-
-def test_coxph_forestplot(mimic_2, check_same_image):
-    adata_subset = mimic_2[:, ["mort_day_censored", "censor_flg", "gender_num", "afib_flg", "day_icu_intime_num"]]
-    coxph = ep.tl.cox_ph(adata_subset, duration_col="mort_day_censored", event_col="censor_flg")
-    fig, ax = ep.pl.cox_ph_forestplot(coxph, fig_size=(12, 3), t_adjuster=0.15, marker="o", size=2, text_size=14)
-
-    check_same_image(
-        fig=fig,
-        base_path=f"{_TEST_IMAGE_PATH}/coxph_forestplot",
-        tol=2e-1,
-    )
diff --git a/tests/plot/test_survival_analysis.py b/tests/plot/test_survival_analysis.py
new file mode 100644
index 00000000..982bc7a8
--- /dev/null
+++ b/tests/plot/test_survival_analysis.py
@@ -0,0 +1,17 @@
+from pathlib import Path
+
+import ehrapy as ep
+
+CURRENT_DIR = Path(__file__).parent
+_TEST_IMAGE_PATH = f"{CURRENT_DIR}/_images"
+
+def test_coxph_forestplot(mimic_2, check_same_image):
+    adata_subset = mimic_2[:, ["mort_day_censored", "censor_flg", "gender_num", "afib_flg", "day_icu_intime_num"]]
+    coxph = ep.tl.cox_ph(adata_subset, duration_col="mort_day_censored", event_col="censor_flg")
+    fig, ax = ep.pl.cox_ph_forestplot(coxph, fig_size=(12, 3), t_adjuster=0.15, marker="o", size=2, text_size=14)
+
+    check_same_image(
+        fig=fig,
+        base_path=f"{_TEST_IMAGE_PATH}/coxph_forestplot",
+        tol=2e-1,
+    )
\ No newline at end of file

From 21086812150e4dbe5596d8f7252e6002a59147b3 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 13 Dec 2024 09:01:21 +0000
Subject: [PATCH 14/19] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 ehrapy/plot/_survival_analysis.py    | 12 ++++++++++--
 tests/plot/test_catplot.py           |  1 -
 tests/plot/test_survival_analysis.py |  3 ++-
 3 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/ehrapy/plot/_survival_analysis.py b/ehrapy/plot/_survival_analysis.py
index 6dacc124..3e7c245f 100644
--- a/ehrapy/plot/_survival_analysis.py
+++ b/ehrapy/plot/_survival_analysis.py
@@ -370,7 +370,13 @@ def cox_ph_forestplot(
                 tval.append(
                     [
                         coxph_summary[auc_col][i],
-                        ("(" + str(coxph_summary["coef lower 95%"][i]) + ", " + str(coxph_summary["coef upper 95%"][i]) + ")"),
+                        (
+                            "("
+                            + str(coxph_summary["coef lower 95%"][i])
+                            + ", "
+                            + str(coxph_summary["coef upper 95%"][i])
+                            + ")"
+                        ),
                     ]
                 )
             ytick.append(i)
@@ -401,7 +407,9 @@ def cox_ph_forestplot(
         linewidth=0,
         elinewidth=1,
     )
-    plot.scatter(coxph_summary[auc_col], coxph_summary.index, c=color, s=(size * 25), marker=marker, zorder=3, edgecolors="None")
+    plot.scatter(
+        coxph_summary[auc_col], coxph_summary.index, c=color, s=(size * 25), marker=marker, zorder=3, edgecolors="None"
+    )
     plot.xaxis.set_ticks_position("bottom")
     plot.yaxis.set_ticks_position("left")
     plot.get_xaxis().set_major_formatter(ticker.ScalarFormatter())
diff --git a/tests/plot/test_catplot.py b/tests/plot/test_catplot.py
index 8e569928..e3591132 100644
--- a/tests/plot/test_catplot.py
+++ b/tests/plot/test_catplot.py
@@ -14,4 +14,3 @@ def test_catplot_vanilla(adata_mini, check_same_image):
         base_path=f"{_TEST_IMAGE_PATH}/catplot_vanilla",
         tol=2e-1,
     )
-
diff --git a/tests/plot/test_survival_analysis.py b/tests/plot/test_survival_analysis.py
index 982bc7a8..5196ddad 100644
--- a/tests/plot/test_survival_analysis.py
+++ b/tests/plot/test_survival_analysis.py
@@ -5,6 +5,7 @@
 CURRENT_DIR = Path(__file__).parent
 _TEST_IMAGE_PATH = f"{CURRENT_DIR}/_images"
 
+
 def test_coxph_forestplot(mimic_2, check_same_image):
     adata_subset = mimic_2[:, ["mort_day_censored", "censor_flg", "gender_num", "afib_flg", "day_icu_intime_num"]]
     coxph = ep.tl.cox_ph(adata_subset, duration_col="mort_day_censored", event_col="censor_flg")
@@ -14,4 +15,4 @@ def test_coxph_forestplot(mimic_2, check_same_image):
         fig=fig,
         base_path=f"{_TEST_IMAGE_PATH}/coxph_forestplot",
         tol=2e-1,
-    )
\ No newline at end of file
+    )

From 88e18a7da617f795ce2ba1478044e4db77eaad1d Mon Sep 17 00:00:00 2001
From: Carl Buchholz <32228189+aGuyLearning@users.noreply.github.com>
Date: Fri, 13 Dec 2024 10:33:27 +0100
Subject: [PATCH 15/19] made anything after coxphfitter keyword only

---
 ehrapy/plot/_survival_analysis.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/ehrapy/plot/_survival_analysis.py b/ehrapy/plot/_survival_analysis.py
index 3e7c245f..fdb9c9c2 100644
--- a/ehrapy/plot/_survival_analysis.py
+++ b/ehrapy/plot/_survival_analysis.py
@@ -303,6 +303,7 @@ def kaplan_meier(
 
 def cox_ph_forestplot(
     cox_ph: CoxPHFitter,
+    *,
     labels: list[str] | None = None,
     fig_size: tuple = (10, 10),
     t_adjuster: float = 0.1,

From 613be89b6ce3449f21255182b437447942c3d0ee Mon Sep 17 00:00:00 2001
From: Carl Buchholz <32228189+aGuyLearning@users.noreply.github.com>
Date: Fri, 13 Dec 2024 10:37:42 +0100
Subject: [PATCH 16/19] changed type to iterable

---
 ehrapy/plot/_survival_analysis.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/ehrapy/plot/_survival_analysis.py b/ehrapy/plot/_survival_analysis.py
index fdb9c9c2..10af4537 100644
--- a/ehrapy/plot/_survival_analysis.py
+++ b/ehrapy/plot/_survival_analysis.py
@@ -13,7 +13,7 @@
 from ehrapy.plot import scatter
 
 if TYPE_CHECKING:
-    from collections.abc import Sequence
+    from collections.abc import Iterable, Sequence
     from xmlrpc.client import Boolean
 
     from anndata import AnnData
@@ -304,7 +304,7 @@ def kaplan_meier(
 def cox_ph_forestplot(
     cox_ph: CoxPHFitter,
     *,
-    labels: list[str] | None = None,
+    labels: Iterable[str] | None = None,
     fig_size: tuple = (10, 10),
     t_adjuster: float = 0.1,
     ecolor: str = "dimgray",

From 8c3d17054544db0e31d7746f44209495917ca7b2 Mon Sep 17 00:00:00 2001
From: Carl Buchholz <32228189+aGuyLearning@users.noreply.github.com>
Date: Fri, 13 Dec 2024 10:41:53 +0100
Subject: [PATCH 17/19] added title and show args

---
 ehrapy/plot/_survival_analysis.py | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/ehrapy/plot/_survival_analysis.py b/ehrapy/plot/_survival_analysis.py
index 10af4537..fc513cd6 100644
--- a/ehrapy/plot/_survival_analysis.py
+++ b/ehrapy/plot/_survival_analysis.py
@@ -313,6 +313,8 @@ def cox_ph_forestplot(
     decimal: int = 2,
     text_size: int = 12,
     color: str = "k",
+    show: bool = True,
+    title: str | None = None,
 ):
     """Generates a forest plot to visualize the coefficients and confidence intervals of a Cox Proportional Hazards model.
     The method requires a fitted CoxPHFitter object from the lifelines library.
@@ -330,6 +332,8 @@ def cox_ph_forestplot(
         decimal: Number of decimal places to display.
         text_size: Font size of the text.
         color: Color of the markers.
+        show: Show the plot, do not return axis.
+        title: Set the title of the plot.
 
     Examples:
         >>> import ehrapy as ep
@@ -389,7 +393,7 @@ def cox_ph_forestplot(
 
     x_axis_lower_bound = round(((pd.to_numeric(coxph_summary["coef lower 95%"])).min() - 0.1), 1)
 
-    fig = plt.figure(figsize=fig_size)
+    plt.figure(figsize=fig_size)
     gspec = gridspec.GridSpec(1, 6)
     plot = plt.subplot(gspec[0, 0:4])  # plot of data
     tabl = plt.subplot(gspec[0, 4:])  # table
@@ -434,4 +438,12 @@ def cox_ph_forestplot(
     plot.spines["top"].set_visible(False)
     plot.spines["right"].set_visible(False)
     plot.spines["left"].set_visible(False)
-    return fig, plot
+
+    if title:
+        plt.title(title)
+
+    if not show:
+        return plot
+
+    else:
+        return None

From b3a7c2193462d2fa9926bfc01e77ba34665b0931 Mon Sep 17 00:00:00 2001
From: Carl Buchholz <32228189+aGuyLearning@users.noreply.github.com>
Date: Fri, 13 Dec 2024 10:57:51 +0100
Subject: [PATCH 18/19] less ambiguous loop index

---
 ehrapy/plot/_survival_analysis.py | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/ehrapy/plot/_survival_analysis.py b/ehrapy/plot/_survival_analysis.py
index fc513cd6..3dd3c343 100644
--- a/ehrapy/plot/_survival_analysis.py
+++ b/ehrapy/plot/_survival_analysis.py
@@ -352,21 +352,21 @@ def cox_ph_forestplot(
         labels = coxph_summary.index
     tval = []
     ytick = []
-    for i in range(len(coxph_summary)):
-        if not np.isnan(coxph_summary[auc_col][i]):
+    for row_index in range(len(coxph_summary)):
+        if not np.isnan(coxph_summary[auc_col][row_index]):
             if (
-                (isinstance(coxph_summary[auc_col][i], float))
-                & (isinstance(coxph_summary["coef lower 95%"][i], float))
-                & (isinstance(coxph_summary["coef upper 95%"][i], float))
+                (isinstance(coxph_summary[auc_col][row_index], float))
+                & (isinstance(coxph_summary["coef lower 95%"][row_index], float))
+                & (isinstance(coxph_summary["coef upper 95%"][row_index], float))
             ):
                 tval.append(
                     [
-                        round(coxph_summary[auc_col][i], decimal),
+                        round(coxph_summary[auc_col][row_index], decimal),
                         (
                             "("
-                            + str(round(coxph_summary["coef lower 95%"][i], decimal))
+                            + str(round(coxph_summary["coef lower 95%"][row_index], decimal))
                             + ", "
-                            + str(round(coxph_summary["coef upper 95%"][i], decimal))
+                            + str(round(coxph_summary["coef upper 95%"][row_index], decimal))
                             + ")"
                         ),
                     ]
@@ -374,20 +374,20 @@ def cox_ph_forestplot(
             else:
                 tval.append(
                     [
-                        coxph_summary[auc_col][i],
+                        coxph_summary[auc_col][row_index],
                         (
                             "("
-                            + str(coxph_summary["coef lower 95%"][i])
+                            + str(coxph_summary["coef lower 95%"][row_index])
                             + ", "
-                            + str(coxph_summary["coef upper 95%"][i])
+                            + str(coxph_summary["coef upper 95%"][row_index])
                             + ")"
                         ),
                     ]
                 )
-            ytick.append(i)
+            ytick.append(row_index)
         else:
             tval.append([" ", " "])
-            ytick.append(i)
+            ytick.append(row_index)
 
     x_axis_upper_bound = round(((pd.to_numeric(coxph_summary["coef upper 95%"])).max() + 0.1), 2)
 

From cfdb1cc35edb43e527700bf17a46a2204be3402b Mon Sep 17 00:00:00 2001
From: Carl Buchholz <32228189+aGuyLearning@users.noreply.github.com>
Date: Fri, 13 Dec 2024 11:13:16 +0100
Subject: [PATCH 19/19] fixed test. had to return figure and axis, so the test
 can save the image

---
 ehrapy/plot/_survival_analysis.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/ehrapy/plot/_survival_analysis.py b/ehrapy/plot/_survival_analysis.py
index 3dd3c343..5230ed1a 100644
--- a/ehrapy/plot/_survival_analysis.py
+++ b/ehrapy/plot/_survival_analysis.py
@@ -313,7 +313,7 @@ def cox_ph_forestplot(
     decimal: int = 2,
     text_size: int = 12,
     color: str = "k",
-    show: bool = True,
+    show: bool = None,
     title: str | None = None,
 ):
     """Generates a forest plot to visualize the coefficients and confidence intervals of a Cox Proportional Hazards model.
@@ -332,7 +332,7 @@ def cox_ph_forestplot(
         decimal: Number of decimal places to display.
         text_size: Font size of the text.
         color: Color of the markers.
-        show: Show the plot, do not return axis.
+        show: Show the plot, do not return figure and axis.
         title: Set the title of the plot.
 
     Examples:
@@ -393,7 +393,7 @@ def cox_ph_forestplot(
 
     x_axis_lower_bound = round(((pd.to_numeric(coxph_summary["coef lower 95%"])).min() - 0.1), 1)
 
-    plt.figure(figsize=fig_size)
+    fig = plt.figure(figsize=fig_size)
     gspec = gridspec.GridSpec(1, 6)
     plot = plt.subplot(gspec[0, 0:4])  # plot of data
     tabl = plt.subplot(gspec[0, 4:])  # table
@@ -443,7 +443,7 @@ def cox_ph_forestplot(
         plt.title(title)
 
     if not show:
-        return plot
+        return fig, plot
 
     else:
         return None