Render plot used everywhere

.gitignore

@@ -4,6 +4,7 @@ wandb/
 *slurm*
 tests/data/genomes
 tests/data/test_pipeline
+tests/data/pl_output/
 
 # Sphinx documentation
 _build
@@ -12,4 +13,4 @@ node_modules
 .DS_Store
 ._.DS_Store
 docs/tutorials/mouse_biccn.ipynb
-docs/tutorials/.ipynb_checkpoints
+docs/tutorials/.ipynb_checkpoints

pyproject.toml

@@ -65,6 +65,7 @@ test = [
     "coverage",
     "anndata",
     "genomepy",
+    "modisco-lite",
 ]
 
 [tool.coverage.run]

src/crested/pl/_utils.py

@@ -7,6 +7,7 @@
 
 def render_plot(
     fig,
+    ax=None,
     width: int = 8,
     height: int = 8,
     title: str | None = None,
@@ -36,6 +37,8 @@ def render_plot(
     ----------
     fig
         The figure object to render.
+    ax
+        The axis object to which to apply the customizations. If None, all axes in the figure are modified.
     width
         Width of the plot (inches).
     height
@@ -78,7 +81,9 @@ def render_plot(
         fig.supxlabel(supxlabel)
     if supylabel:
         fig.supylabel(supylabel)
-    for ax in fig.axes:
+    axes_to_modify = [ax] if ax else fig.axes
+
+    for ax in axes_to_modify:
         if xlabel:
             ax.set_xlabel(xlabel, fontsize=x_label_fontsize)
         if ylabel:
@@ -89,6 +94,7 @@ def render_plot(
         for label in ax.get_yticklabels():
             label.set_fontsize(y_tick_fontsize)
             label.set_rotation(y_label_rotation)
+
     if tight_rect:
         plt.tight_layout(rect=tight_rect)
     else:

src/crested/pl/hist/_locus_scoring.py

@@ -5,16 +5,17 @@
 import matplotlib.pyplot as plt
 import numpy as np
 
+from crested.pl._utils import render_plot
+
 
 def locus_scoring(
     scores: np.ndarray,
     range: tuple[int, int],
     gene_start: int | None = None,
     gene_end: int | None = None,
-    title: str = "Predictions across Genomic Regions",
     bigwig_values: np.ndarray | None = None,
     bigwig_midpoints: list[int] | None = None,
-    filename: str | None = None,
+    **kwargs,
 ):
     """
     Plot the predictions as a line chart over the entire genomic input and optionally indicate the gene locus.
@@ -33,14 +34,14 @@ def locus_scoring(
         The start position of the gene locus to highlight on the plot.
     gene_end
         The end position of the gene locus to highlight on the plot.
-    title
-        The title of the plot.
     bigwig_values
         A numpy array of values extracted from a bigWig file for the same coordinates.
     bigwig_midpoints
         A list of base pair positions corresponding to the bigwig_values.
-    filename
-        The filename to save the plot to.
+    kwargs
+        Additional arguments passed to :func:`~crested.pl.render_plot` to
+        control the final plot output. Please see :func:`~crested.pl.render_plot`
+        for details.
 
     See Also
     --------
@@ -61,12 +62,20 @@ def locus_scoring(
 
     .. image:: ../../../../docs/_static/img/examples/hist_locus_scoring.png
     """
-    # Plotting predictions
-    plt.figure(figsize=(30, 10))
-
     # Top plot: Model predictions
-    plt.subplot(2, 1, 1)
-    plt.plot(
+    if bigwig_midpoints is not None and bigwig_values is not None:
+        nrows = 2
+    else:
+        nrows = 1
+    fig, axes = plt.subplots(
+        nrows,
+        1,
+        sharex=True,
+    )
+    if nrows == 1:
+        axes = [axes]
+
+    axes[0].plot(
         np.arange(range[0], range[1]),
         scores,
         marker="o",
@@ -75,37 +84,46 @@ def locus_scoring(
         label="Prediction Score",
     )
     if gene_start is not None and gene_end is not None:
-        plt.axvspan(gene_start, gene_end, color="red", alpha=0.3, label="Gene Locus")
-    plt.title(title)
-    plt.xlabel("Genomic Position")
-    plt.ylabel("Prediction Score")
-    plt.ylim(bottom=0)
-    plt.xticks(rotation=90)
-    plt.grid(True)
-    plt.legend()
+        axes[0].axvspan(
+            gene_start, gene_end, color="red", alpha=0.3, label="Gene Locus"
+        )
+
+    axes[0].set_xlabel("Genomic Position")
+    for label in axes[0].get_xticklabels():
+        label.set_rotation(90)
+    axes[0].set_ylabel("Prediction Score")
+    axes[0].set_ylim(bottom=0)
+    axes[0].grid(True)
+    axes[0].legend()
 
     # Bottom plot: bigWig values
     if bigwig_values is not None and bigwig_midpoints is not None:
-        plt.subplot(2, 1, 2)
-        plt.plot(
+        axes[1].plot(
             bigwig_midpoints,
             bigwig_values,
             linestyle="-",
             color="g",
             label="bigWig Values",
         )
         if gene_start is not None and gene_end is not None:
-            plt.axvspan(
+            axes[1].axvspan(
                 gene_start, gene_end, color="red", alpha=0.3, label="Gene Locus"
             )
-        plt.xlabel("Genomic Position")
-        plt.ylabel("bigWig Values")
-        plt.xticks(rotation=90)
-        plt.ylim(bottom=0)
-        plt.grid(True)
-        plt.legend()
+        axes[1].set_xlabel("Genomic Position")
+        axes[1].set_ylabel("bigWig Values")
+        axes[1].grid(True)
+        axes[1].legend()
 
     plt.tight_layout()
-    if filename:
-        plt.savefig(filename)
-    plt.show()
+
+    default_height = 5 * nrows
+    default_width = 30
+
+    if "width" not in kwargs:
+        kwargs["width"] = default_width
+    if "height" not in kwargs:
+        kwargs["height"] = default_height
+    if "title" not in kwargs:
+        kwargs["title"] = "Predictions across Genomic Regions"
+
+    return render_plot(fig, **kwargs)

src/crested/pl/patterns/__init__.py

@@ -14,7 +14,7 @@
 def _optional_function_warning(*args, **kwargs):
     logger.error(
         "The requested functionality requires the 'tfmodisco' package, which is not installed. "
-        "Please install it with `pip install crested[tfmodisco]`.",
+        "Please install it with `pip install modisco-lite`.",
     )