smftools 0.2.5__py3-none-any.whl → 0.3.1__py3-none-any.whl

smftools/plotting/__init__.py

@@ -1,32 +1,42 @@
-from .autocorrelation_plotting import *
-from .classifiers import (
-    plot_feature_importances_or_saliency,
-    plot_model_curves_from_adata,
-    plot_model_curves_from_adata_with_frequency_grid,
-    plot_model_performance,
-)
-from .general_plotting import (
-    combined_hmm_raw_clustermap,
-    combined_raw_clustermap,
-    plot_hmm_layers_rolling_by_sample_ref,
-)
-from .hmm_plotting import *
-from .position_stats import (
-    plot_bar_relative_risk,
-    plot_positionwise_matrix,
-    plot_positionwise_matrix_grid,
-    plot_volcano_relative_risk,
-)
-from .qc_plotting import *
+from __future__ import annotations
 
-__all__ = [
-    "combined_hmm_raw_clustermap",
-    "plot_bar_relative_risk",
-    "plot_positionwise_matrix",
-    "plot_positionwise_matrix_grid",
-    "plot_volcano_relative_risk",
-    "plot_feature_importances_or_saliency",
-    "plot_model_performance",
-    "plot_model_curves_from_adata",
-    "plot_model_curves_from_adata_with_frequency_grid",
-]
+from importlib import import_module
+
+_LAZY_ATTRS = {
+    "combined_hmm_length_clustermap": "smftools.plotting.general_plotting",
+    "combined_hmm_raw_clustermap": "smftools.plotting.general_plotting",
+    "combined_raw_clustermap": "smftools.plotting.general_plotting",
+    "plot_rolling_nn_and_layer": "smftools.plotting.general_plotting",
+    "plot_hmm_layers_rolling_by_sample_ref": "smftools.plotting.general_plotting",
+    "plot_nmf_components": "smftools.plotting.general_plotting",
+    "plot_cp_sequence_components": "smftools.plotting.general_plotting",
+    "plot_embedding": "smftools.plotting.general_plotting",
+    "plot_read_span_quality_clustermaps": "smftools.plotting.general_plotting",
+    "plot_pca": "smftools.plotting.general_plotting",
+    "plot_sequence_integer_encoding_clustermaps": "smftools.plotting.general_plotting",
+    "plot_umap": "smftools.plotting.general_plotting",
+    "plot_bar_relative_risk": "smftools.plotting.position_stats",
+    "plot_positionwise_matrix": "smftools.plotting.position_stats",
+    "plot_positionwise_matrix_grid": "smftools.plotting.position_stats",
+    "plot_volcano_relative_risk": "smftools.plotting.position_stats",
+    "plot_feature_importances_or_saliency": "smftools.plotting.classifiers",
+    "plot_model_curves_from_adata": "smftools.plotting.classifiers",
+    "plot_model_curves_from_adata_with_frequency_grid": "smftools.plotting.classifiers",
+    "plot_model_performance": "smftools.plotting.classifiers",
+    "plot_read_qc_histograms": "smftools.plotting.qc_plotting",
+    "plot_rolling_grid": "smftools.plotting.autocorrelation_plotting",
+    "plot_spatial_autocorr_grid": "smftools.plotting.autocorrelation_plotting",
+    "plot_hmm_size_contours": "smftools.plotting.hmm_plotting",
+}
+
+
+def __getattr__(name: str):
+    if name in _LAZY_ATTRS:
+        module = import_module(_LAZY_ATTRS[name])
+        attr = getattr(module, name)
+        globals()[name] = attr
+        return attr
+    raise AttributeError(f"module '{__name__}' has no attribute '{name}'")
+
+
+__all__ = list(_LAZY_ATTRS.keys())

smftools/plotting/autocorrelation_plotting.py

@@ -1,8 +1,12 @@
+from __future__ import annotations
+
 from typing import Optional
 
 import numpy as np
 import pandas as pd
 
+from smftools.optional_imports import require
+
 
 def plot_spatial_autocorr_grid(
     adata,
@@ -35,7 +39,7 @@ def plot_spatial_autocorr_grid(
     import os
     import warnings
 
-    import matplotlib.pyplot as plt
+    plt = require("matplotlib.pyplot", extra="plotting", purpose="autocorrelation plots")
 
     # Try importing analyzer (used only as fallback)
     try:
@@ -518,7 +522,7 @@ def plot_rolling_metrics(df, out_png=None, title=None, figsize=(10, 3.5), dpi=16
     Plot NRL and SNR vs window center from the dataframe returned by rolling_autocorr_metrics.
     If out_png is None, returns the matplotlib Figure object; otherwise saves PNG and returns path.
     """
-    import matplotlib.pyplot as plt
+    plt = require("matplotlib.pyplot", extra="plotting", purpose="autocorrelation plots")
 
     # sort by center
     df2 = df.sort_values("center")
@@ -543,12 +547,12 @@ def plot_rolling_metrics(df, out_png=None, title=None, figsize=(10, 3.5), dpi=16
     if out_png:
         fig.savefig(out_png, bbox_inches="tight")
         if not show:
-            import matplotlib
+            matplotlib = require("matplotlib", extra="plotting", purpose="autocorrelation plots")
 
             matplotlib.pyplot.close(fig)
         return out_png
     if not show:
-        import matplotlib
+        matplotlib = require("matplotlib", extra="plotting", purpose="autocorrelation plots")
 
         matplotlib.pyplot.close(fig)
     return fig
@@ -600,7 +604,7 @@ def plot_rolling_grid(
     """
     import os
 
-    import matplotlib.pyplot as plt
+    plt = require("matplotlib.pyplot", extra="plotting", purpose="autocorrelation plots")
 
     if per_metric_ylim is None:
         per_metric_ylim = {}

smftools/plotting/classifiers.py

@@ -1,8 +1,13 @@
+from __future__ import annotations
+
 import os
 
-import matplotlib.pyplot as plt
 import numpy as np
-import torch
+
+from smftools.optional_imports import require
+
+plt = require("matplotlib.pyplot", extra="plotting", purpose="model plots")
+torch = require("torch", extra="ml-base", purpose="model saliency plots")
 
 
 def plot_model_performance(metrics, save_path=None):
@@ -260,7 +265,10 @@ def plot_model_curves_from_adata(
         ylim_roc: Y-axis limits for ROC curve.
         ylim_pr: Y-axis limits for PR curve.
     """
-    from sklearn.metrics import auc, precision_recall_curve, roc_curve
+    sklearn_metrics = require("sklearn.metrics", extra="ml-base", purpose="model curves")
+    auc = sklearn_metrics.auc
+    precision_recall_curve = sklearn_metrics.precision_recall_curve
+    roc_curve = sklearn_metrics.roc_curve
 
     if omit_training:
         subset = adata[~adata.obs["used_for_training"].astype(bool)]
@@ -349,7 +357,11 @@ def plot_model_curves_from_adata_with_frequency_grid(
     import os
 
     import numpy as np
-    from sklearn.metrics import auc, precision_recall_curve, roc_curve
+
+    sklearn_metrics = require("sklearn.metrics", extra="ml-base", purpose="model curves")
+    auc = sklearn_metrics.auc
+    precision_recall_curve = sklearn_metrics.precision_recall_curve
+    roc_curve = sklearn_metrics.roc_curve
 
     if f1_levels is None:
         f1_levels = np.linspace(0.2, 0.9, 8)