RNAvigate 1.1.0__tar.gz

rnavigate-1.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2021 Patrick Irving and the Weeks Lab at The University of North Carolina at Chapel Hill
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

rnavigate-1.1.0/PKG-INFO

@@ -0,0 +1,75 @@
+Metadata-Version: 2.4
+Name: RNAvigate
+Version: 1.1.0
+Summary: RNA visualization and graphical analysis toolset
+Author-email: Patrick Irving <psirving@gmail.com>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/Weeks-UNC/RNAvigate
+Project-URL: Documentation, https://rnavigate.readthedocs.io/en/latest/
+Project-URL: Bug Tracker, https://github.com/Weeks-UNC/RNAvigate/issues
+Keywords: RNA,chemical probing,visualization,bioinformatics,structural biology
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Classifier: Intended Audience :: Science/Research
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: biopython>=1.78
+Requires-Dist: ipython>=8.18.1
+Requires-Dist: jedi>=0.19.2
+Requires-Dist: matplotlib>=3.8
+Requires-Dist: numpy>=1.20.1
+Requires-Dist: openpyxl>=3.1.2
+Requires-Dist: pandas>=1.4.4
+Requires-Dist: py3dmol>=2.0.0
+Requires-Dist: requests
+Requires-Dist: scikit-learn>=1.0.2
+Requires-Dist: scipy>=1.6.2
+Requires-Dist: seaborn>=0.13.0
+Requires-Dist: statsmodels>=0.14.1
+Provides-Extra: dev
+Requires-Dist: ipykernel>=6.6.0; extra == "dev"
+Requires-Dist: jupyter>=1.0.0; extra == "dev"
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: pytest-cov>=4.0; extra == "dev"
+Requires-Dist: ruff>=0.4; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: sphinx-autobuild; extra == "docs"
+Requires-Dist: sphinx-rtd-theme; extra == "docs"
+Requires-Dist: nbsphinx; extra == "docs"
+Dynamic: license-file
+
+RNAvigate
+=========
+
+RNAvigate is a toolset to explore, compare, and visualize chemical probing data,
+structure models, and annotations between experimental samples.
+
+**For non-coders**, RNAvigate is designed to be easy to learn. Reach out to me if you
+want help onboarding for your group. Using RNAvigate in a Jupyter Notebook will
+transform how you explore data, document thoughts, and share transparent and reproducible analyses.
+
+**For coders**, RNAvigate is extremely flexible and a great package for scripting
+and standardizing plots and analyses as part of a bigger workflow.
+
+* [**_Click here for the full documentation_**](https://rnavigate.readthedocs.io/en/latest/)
+
+## Reach out
+
+Coders and non-coders, **reach out** if you have any comments or issues at all!
+I love to help users and to learn how you are using this tool.
+
+Please, use GitHub Issues **_liberally_** or email me. "Issues" can be:
+
+- a "dumb" question (my favorite kind) or a complicated one.
+- *any* comment or suggestion for the documentation or the code.
+- a cool thing that you did with RNAvigate.
+- a report of a bug or unclear error.
+- a request for help on acheiving a desired vizualization or analysis.
+- a request for advice on any chemical probing matter.

rnavigate-1.1.0/README.md

@@ -0,0 +1,28 @@
+RNAvigate
+=========
+
+RNAvigate is a toolset to explore, compare, and visualize chemical probing data,
+structure models, and annotations between experimental samples.
+
+**For non-coders**, RNAvigate is designed to be easy to learn. Reach out to me if you
+want help onboarding for your group. Using RNAvigate in a Jupyter Notebook will
+transform how you explore data, document thoughts, and share transparent and reproducible analyses.
+
+**For coders**, RNAvigate is extremely flexible and a great package for scripting
+and standardizing plots and analyses as part of a bigger workflow.
+
+* [**_Click here for the full documentation_**](https://rnavigate.readthedocs.io/en/latest/)
+
+## Reach out
+
+Coders and non-coders, **reach out** if you have any comments or issues at all!
+I love to help users and to learn how you are using this tool.
+
+Please, use GitHub Issues **_liberally_** or email me. "Issues" can be:
+
+- a "dumb" question (my favorite kind) or a complicated one.
+- *any* comment or suggestion for the documentation or the code.
+- a cool thing that you did with RNAvigate.
+- a report of a bug or unclear error.
+- a request for help on acheiving a desired vizualization or analysis.
+- a request for advice on any chemical probing matter.

rnavigate-1.1.0/RNAvigate.egg-info/PKG-INFO

@@ -0,0 +1,75 @@
+Metadata-Version: 2.4
+Name: RNAvigate
+Version: 1.1.0
+Summary: RNA visualization and graphical analysis toolset
+Author-email: Patrick Irving <psirving@gmail.com>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/Weeks-UNC/RNAvigate
+Project-URL: Documentation, https://rnavigate.readthedocs.io/en/latest/
+Project-URL: Bug Tracker, https://github.com/Weeks-UNC/RNAvigate/issues
+Keywords: RNA,chemical probing,visualization,bioinformatics,structural biology
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Classifier: Intended Audience :: Science/Research
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: biopython>=1.78
+Requires-Dist: ipython>=8.18.1
+Requires-Dist: jedi>=0.19.2
+Requires-Dist: matplotlib>=3.8
+Requires-Dist: numpy>=1.20.1
+Requires-Dist: openpyxl>=3.1.2
+Requires-Dist: pandas>=1.4.4
+Requires-Dist: py3dmol>=2.0.0
+Requires-Dist: requests
+Requires-Dist: scikit-learn>=1.0.2
+Requires-Dist: scipy>=1.6.2
+Requires-Dist: seaborn>=0.13.0
+Requires-Dist: statsmodels>=0.14.1
+Provides-Extra: dev
+Requires-Dist: ipykernel>=6.6.0; extra == "dev"
+Requires-Dist: jupyter>=1.0.0; extra == "dev"
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: pytest-cov>=4.0; extra == "dev"
+Requires-Dist: ruff>=0.4; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: sphinx-autobuild; extra == "docs"
+Requires-Dist: sphinx-rtd-theme; extra == "docs"
+Requires-Dist: nbsphinx; extra == "docs"
+Dynamic: license-file
+
+RNAvigate
+=========
+
+RNAvigate is a toolset to explore, compare, and visualize chemical probing data,
+structure models, and annotations between experimental samples.
+
+**For non-coders**, RNAvigate is designed to be easy to learn. Reach out to me if you
+want help onboarding for your group. Using RNAvigate in a Jupyter Notebook will
+transform how you explore data, document thoughts, and share transparent and reproducible analyses.
+
+**For coders**, RNAvigate is extremely flexible and a great package for scripting
+and standardizing plots and analyses as part of a bigger workflow.
+
+* [**_Click here for the full documentation_**](https://rnavigate.readthedocs.io/en/latest/)
+
+## Reach out
+
+Coders and non-coders, **reach out** if you have any comments or issues at all!
+I love to help users and to learn how you are using this tool.
+
+Please, use GitHub Issues **_liberally_** or email me. "Issues" can be:
+
+- a "dumb" question (my favorite kind) or a complicated one.
+- *any* comment or suggestion for the documentation or the code.
+- a cool thing that you did with RNAvigate.
+- a report of a bug or unclear error.
+- a request for help on acheiving a desired vizualization or analysis.
+- a request for advice on any chemical probing matter.

rnavigate-1.1.0/RNAvigate.egg-info/SOURCES.txt

@@ -0,0 +1,61 @@
+LICENSE
+README.md
+pyproject.toml
+RNAvigate.egg-info/PKG-INFO
+RNAvigate.egg-info/SOURCES.txt
+RNAvigate.egg-info/dependency_links.txt
+RNAvigate.egg-info/requires.txt
+RNAvigate.egg-info/top_level.txt
+rnavigate/__init__.py
+rnavigate/data_loading.py
+rnavigate/helper_functions.py
+rnavigate/plotting_functions.py
+rnavigate/rnavigate.py
+rnavigate/styles.py
+rnavigate/analysis/__init__.py
+rnavigate/analysis/auroc.py
+rnavigate/analysis/check_sequence.py
+rnavigate/analysis/deltashape.py
+rnavigate/analysis/fragmapper.py
+rnavigate/analysis/logcompare.py
+rnavigate/analysis/lowss.py
+rnavigate/data/__init__.py
+rnavigate/data/alignments.py
+rnavigate/data/annotation.py
+rnavigate/data/colors.py
+rnavigate/data/data.py
+rnavigate/data/interactions.py
+rnavigate/data/pdb.py
+rnavigate/data/profile.py
+rnavigate/data/secondary_structure.py
+rnavigate/examples/__init__.py
+rnavigate/examples/rmrp_data/__init__.py
+rnavigate/examples/rnasep_data/__init__.py
+rnavigate/examples/rrna_fragmap_data/__init__.py
+rnavigate/examples/tpp_data/__init__.py
+rnavigate/plots/__init__.py
+rnavigate/plots/alignment.py
+rnavigate/plots/arc.py
+rnavigate/plots/circle.py
+rnavigate/plots/disthist.py
+rnavigate/plots/heatmap.py
+rnavigate/plots/linreg.py
+rnavigate/plots/mol.py
+rnavigate/plots/ntdist.py
+rnavigate/plots/plots.py
+rnavigate/plots/profile.py
+rnavigate/plots/qc.py
+rnavigate/plots/roc.py
+rnavigate/plots/skyline.py
+rnavigate/plots/sm.py
+rnavigate/plots/ss.py
+rnavigate/plots/functions/__init__.py
+rnavigate/plots/functions/circle.py
+rnavigate/plots/functions/functions.py
+rnavigate/plots/functions/ss.py
+rnavigate/plots/functions/tracks.py
+rnavigate/transcriptomics/__init__.py
+rnavigate/transcriptomics/bed.py
+rnavigate/transcriptomics/eclip.py
+rnavigate/transcriptomics/transcriptome.py
+tests/test_import.py

rnavigate-1.1.0/RNAvigate.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

rnavigate-1.1.0/RNAvigate.egg-info/requires.txt

@@ -0,0 +1,26 @@
+biopython>=1.78
+ipython>=8.18.1
+jedi>=0.19.2
+matplotlib>=3.8
+numpy>=1.20.1
+openpyxl>=3.1.2
+pandas>=1.4.4
+py3dmol>=2.0.0
+requests
+scikit-learn>=1.0.2
+scipy>=1.6.2
+seaborn>=0.13.0
+statsmodels>=0.14.1
+
+[dev]
+ipykernel>=6.6.0
+jupyter>=1.0.0
+pytest>=7.0
+pytest-cov>=4.0
+ruff>=0.4
+
+[docs]
+sphinx
+sphinx-autobuild
+sphinx-rtd-theme
+nbsphinx

rnavigate-1.1.0/RNAvigate.egg-info/top_level.txt

@@ -0,0 +1 @@
+rnavigate

rnavigate-1.1.0/pyproject.toml

@@ -0,0 +1,83 @@
+[build-system]
+requires = ["setuptools>=61", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "RNAvigate"
+version = "1.1.0"
+description = "RNA visualization and graphical analysis toolset"
+readme = "README.md"
+license = "MIT"
+authors = [
+    { name = "Patrick Irving", email = "psirving@gmail.com" },
+]
+keywords = ["RNA", "chemical probing", "visualization", "bioinformatics", "structural biology"]
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Topic :: Scientific/Engineering :: Visualization",
+    "Intended Audience :: Science/Research",
+]
+requires-python = ">=3.9"
+dependencies = [
+    "biopython>=1.78",
+    "ipython>=8.18.1",
+    "jedi>=0.19.2",
+    "matplotlib>=3.8",
+    "numpy>=1.20.1",
+    "openpyxl>=3.1.2",
+    "pandas>=1.4.4",
+    "py3dmol>=2.0.0",
+    "requests",
+    "scikit-learn>=1.0.2",
+    "scipy>=1.6.2",
+    "seaborn>=0.13.0",
+    "statsmodels>=0.14.1",
+]
+
+[project.optional-dependencies]
+dev = [
+    "ipykernel>=6.6.0",
+    "jupyter>=1.0.0",
+    "pytest>=7.0",
+    "pytest-cov>=4.0",
+    "ruff>=0.4",
+]
+docs = [
+    "sphinx",
+    "sphinx-autobuild",
+    "sphinx-rtd-theme",
+    "nbsphinx",
+]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+python_files = ["test_*.py"]
+python_classes = ["Test*"]
+python_functions = ["test_*"]
+
+[project.urls]
+Homepage = "https://github.com/Weeks-UNC/RNAvigate"
+Documentation = "https://rnavigate.readthedocs.io/en/latest/"
+"Bug Tracker" = "https://github.com/Weeks-UNC/RNAvigate/issues"
+
+[tool.ruff]
+target-version = "py39"
+line-length = 88
+exclude = ["docs/"]
+
+[tool.ruff.lint]
+select = ["E", "F", "W", "I"]
+# Some files have load-order-dependent imports due to circular imports that must be
+# resolved before alphabetical sorting can be enforced.
+# See the high-priority "Fix circular imports" item in TODO.md.
+ignore = ["E501", "I001"]  # line-length and import ordering
+
+[tool.ruff.format]
+
+[tool.setuptools.packages.find]
+include = ["rnavigate", "rnavigate.*"]

rnavigate-1.1.0/rnavigate/__init__.py

@@ -0,0 +1,63 @@
+"""RNAvigate
+
+RNA visualization and graphical analysis toolset
+
+A Jupyter-compatible toolset for visually exploring RNA structure and chemical
+probing data.
+"""
+
+from rnavigate.rnavigate import Sample
+from rnavigate.plotting_functions import (
+    plot_options,
+    plot_alignment,
+    plot_arcs,
+    plot_arcs_compare,
+    plot_circle,
+    plot_disthist,
+    plot_heatmap,
+    plot_linreg,
+    plot_mol,
+    plot_ntdist,
+    plot_profile,
+    plot_qc,
+    plot_roc,
+    plot_shapemapper,
+    plot_skyline,
+    plot_ss,
+)
+from rnavigate import analysis
+from rnavigate import data
+from rnavigate import plots
+from rnavigate import styles
+from rnavigate import transcriptomics
+
+__version__ = "1.0.0"
+__author__ = "Patrick S. Irving"
+__email__ = "psirving@email.unc.edu"
+
+__all__ = [
+    "Sample",
+    # plotting functions
+    "plot_options",
+    "plot_alignment",
+    "plot_arcs",
+    "plot_arcs_compare",
+    "plot_circle",
+    "plot_disthist",
+    "plot_heatmap",
+    "plot_linreg",
+    "plot_mol",
+    "plot_ntdist",
+    "plot_profile",
+    "plot_qc",
+    "plot_roc",
+    "plot_shapemapper",
+    "plot_skyline",
+    "plot_ss",
+    # modules
+    "analysis",
+    "data",
+    "plots",
+    "styles",
+    "transcriptomics",
+]

rnavigate-1.1.0/rnavigate/analysis/__init__.py

@@ -0,0 +1,18 @@
+from rnavigate.analysis.logcompare import LogCompare
+from rnavigate.analysis.lowss import LowSS
+from rnavigate.analysis.deltashape import DeltaSHAPE, DeltaSHAPEProfile
+from rnavigate.analysis.auroc import WindowedAUROC
+from rnavigate.analysis.fragmapper import FragMaP, Fragmapper, FragmapperReplicates
+from rnavigate.analysis.check_sequence import SequenceChecker
+
+__all__ = [
+    "LogCompare",
+    "LowSS",
+    "DeltaSHAPE",
+    "DeltaSHAPEProfile",
+    "WindowedAUROC",
+    "FragMaP",
+    "Fragmapper",
+    "FragmapperReplicates",
+    "SequenceChecker",
+]

rnavigate-1.1.0/rnavigate/analysis/auroc.py

@@ -0,0 +1,198 @@
+"""Windowed AUROC assesses agreement between reactivities and base-pairing."""
+
+import numpy as np
+from sklearn.metrics import auc, roc_curve
+
+from rnavigate import plots
+
+
+# TODO: refactor as subclass of rnavigate.Sample
+class WindowedAUROC:
+    """Compute and display windowed AUROC analysis.
+
+    This analysis computes the ROC curve over a sliding window for the
+    performance of per-nucleotide data (usually SHAPE-MaP or DMS-MaP Normalized
+    reactivity) in predicting the base-pairing status of each nucleotide. The
+    area under this curve (AUROC) is displayed compared to the median across
+    the RNA. Below, an arc plot displays the secondary structure and
+    per-nucleotide profile.
+
+     AUROC values (should) range from 0.5 (no predictive power) to 1.0
+    (perfect predictive power). A value of 0.5 indicates that the reactivity
+    profile does not fit the structure prediction well. These regions are good
+    candidates for further investigation with ensemble deconvolution.
+
+    References
+    ----------
+    Lan, T.C.T., Allan, M.F., Malsick, L.E. et al. Secondary structural
+        ensembles of the SARS-CoV-2 RNA genome in infected cells. Nat Commun
+        13, 1128 (2022). https://doi.org/10.1038/s41467-022-28603-2
+
+    Methods
+    -------
+    __init__: Computes the AUROC array and AUROC median.
+    plot_auroc: Displays the AUROC analysis over the given region.
+        Returns Plot object
+
+    Attributes
+    ----------
+    sample : rnavigate.Sample
+        sample to retrieve profile and secondary structure
+    structure : str
+        Data keyword of sample pointing to secondary structure
+        e.g. sample.data[structure]
+    profile : str
+        Data keyword of sample pointing to profile
+        e.g. sample.data[profile]
+    sequence : the sequence string of sample.data[structure]
+    window: the size of the windows
+    nt_length: the length of sequence string
+    auroc: the auroc numpy array, length = nt_length, padded with np.nan
+    median_auroc: the median of the auroc array
+    """
+
+    def __init__(
+        self,
+        sample,
+        window=81,
+        profile="default_profile",
+        structure="default_structure",
+    ):
+        """Compute the AUROC for all windows. AUROC is a measure of how well a
+        reactivity profile predicts paired vs. unpaired nucleotide status.
+
+        Parameters
+        ----------
+        sample : rnav.Sample
+            Your rnavigate sample
+        window : int, optional
+            number of nucleotides to include in window
+            Defaults to 81.
+        profile (str, optional): data keyword of provided sample pointing
+            to a profile.
+            Defaults to "default_profile"
+        structure (str, optional): data keyword of provided sample pointing
+            to a secondary structure.
+            Defaults to "default_structure"
+        """
+        # ensure sample contains profile and structure data
+        for data in [profile, structure]:
+            assert data in sample.data.keys(), f"Sample missing {data} data"
+
+        # store basic information
+        self.sample = sample
+        self.structure = sample.get_data(structure)
+        self.profile = sample.get_data(profile)
+        self.sequence = self.structure.sequence
+        self.window = window
+        self.nt_length = self.structure.length
+
+        # get Norm_profile array and structure array
+        profile = self.profile.data["Norm_profile"].values
+        pair_nts = self.structure.pair_nts
+
+        # for each possible window: compute auroc and populate array
+        self.auroc = np.full(len(profile), np.nan)
+        pad = window // 2
+        for i in range(pad, len(profile) - pad):
+            # get profile and structure values within window
+            win_profile = profile[i - pad : i + pad + 1]
+            win_ct = pair_nts[i - pad : i + pad + 1]
+            # ignore positions where profile is nan
+            valid = ~np.isnan(win_profile)
+            # y: classification (paired or unpaired)
+            y = win_ct[valid] == 0
+            scores = win_profile[valid]
+            # skip this window if there are less than 10 paired or unpaired nts
+            if (sum(y) < 10) or (sum(~y) < 10):
+                continue
+            # add window auroc to array
+            tpr, fpr, _ = roc_curve(y, scores)
+            self.auroc[i] = auc(tpr, fpr)
+
+        self.auroc_median = np.nanmedian(self.auroc)
+
+    def plot_auroc(self, region=None):
+        """Plot the result of the windowed AUROC analysis, with arc plot of
+        structure and reactivity profile.
+
+        Args:
+            region (list of int: length 2, optional): Start and end nucleotide
+                positions to plot. Defaults to [1, RNA length].
+        """
+        if region is None:
+            start = 1
+            stop = self.nt_length
+            region = [start, stop]
+            region_length = self.nt_length
+        else:
+            start, stop = region
+            region_length = stop - start + 1
+
+        plot = plots.AP(1, region_length, cols=1, rows=1, region=region)
+        ax = plot.axes[0, 0]
+
+        # fill between auroc values and median, using secondary ax
+        x_values = np.arange(start, stop + 1)
+        auc_ax = ax.twinx()
+        auc_ax.set_ylim(0.5, 1.6)
+        auc_ax.set_yticks([0.5, self.auroc_median, 1.0])
+        auc_ax.fill_between(
+            x_values,
+            self.auroc[start - 1 : stop],
+            self.auroc_median,
+            fc="0.3",
+            lw=0,
+        )
+        plots.adjust_spines(auc_ax, ["left"])
+        plots.clip_spines(auc_ax, ["left"])
+
+        # add structure and reactivity profile track
+        plot.plot_data(
+            sequence=self.structure,
+            structure=self.structure,
+            structure2=None,
+            interactions=None,
+            interactions2=None,
+            profile=self.profile,
+            label="label",
+            seqbar=False,
+            title=False,
+            annotations=[],
+            plot_error=False,
+        )
+
+        # Place Track Labels
+        ax.set_title(
+            f"{self.sample.sample}\n{start} - {stop}",
+            loc="left",
+            fontdict={"fontsize": 48},
+        )
+        ax.text(
+            1.002,
+            6 / 8,
+            "Secondary\nStructure",
+            transform=ax.transAxes,
+            fontsize=36,
+            va="center",
+        )
+        ax.text(
+            1.002,
+            2 / 8,
+            f"{self.window}-nt window\nAUROC",
+            transform=ax.transAxes,
+            va="center",
+            fontsize=36,
+        )
+
+        # limits, ticks, spines, and grid
+        ax.set_ylim([-305, 315])
+        ax.set_xticks(ticks=[x for x in range(500, stop, 500) if x > start])
+        ax.set_xticks(ticks=[x for x in range(100, stop, 100) if x > start], minor=True)
+        ax.tick_params(axis="x", which="major", labelsize=36)
+        plots.adjust_spines(ax, ["bottom"])
+        ax.grid(axis="x")
+
+        # set figure size so that 100 ax units == 1 inch
+        plot.set_figure_size(height_ax_rel=1 / 100, width_ax_rel=1 / 100)
+        return plot