masster 0.3.10__py3-none-any.whl → 0.3.12__py3-none-any.whl

masster/study/plot.py

@@ -7,148 +7,225 @@ import holoviews as hv
 import numpy as np
 import panel
 import polars as pl
-
-from bokeh.io.export import export_png
-from bokeh.models import ColumnDataSource
-from bokeh.models import HoverTool
-from bokeh.palettes import Turbo256
-from bokeh.plotting import figure
-from bokeh.plotting import output_file
-from bokeh.plotting import show
 from tqdm import tqdm
 
 hv.extension("bokeh")
 
 
-def plot_alignment(self, filename=None):
-    import matplotlib.pyplot as plt
-    import numpy as np
+# Replace any unaliased import that could be shadowed:
+# from bokeh.layouts import row
+from bokeh.layouts import row as bokeh_row
 
-    if self.features_maps is None or len(self.features_maps) == 0:
-        self.load_features()
 
-    feature_maps = self.features_maps
-    ref_index = self.alignment_ref_index
-    if ref_index is None:
-        self.logger.error("No alignment performed yet.")
-        return
+def plot_alignment(self, maps: bool = True, filename: str | None = None, width: int = 450, height: int = 450, markersize: int = 3):
+    """Visualize retention time alignment using two synchronized Bokeh scatter plots.
 
-    fmaps = [
-        feature_maps[ref_index],
-        *feature_maps[:ref_index],
-        *feature_maps[ref_index + 1 :],
-    ]
+    - When ``maps=True`` the function reads ``self.features_maps`` (list of FeatureMap)
+      and builds two side-by-side plots: Original RT (left) and Current/Aligned RT (right).
+    - When ``maps=False`` the function uses ``self.features_df`` and expects an
+      ``rt_original`` column (before) and ``rt`` column (after).
 
-    fig = plt.figure(figsize=(12, 6))
+    Parameters
+    - maps: whether to use feature maps (default True).
+    - filename: optional HTML file path to save the plot.
+    - width/height: pixel size of each subplot.
+    - markersize: base marker size.
 
-    ax = fig.add_subplot(1, 2, 1)
-    ax.set_title("Feature maps before alignment")
-    ax.set_ylabel("m/z")
-    ax.set_xlabel("RT")
+    Returns
+    - Bokeh layout (row) containing the two synchronized plots.
+    """
+    # Local imports so the module can be used even if bokeh isn't needed elsewhere
+    from bokeh.models import ColumnDataSource, HoverTool
+    from bokeh.plotting import figure, show, output_file
+    from bokeh.palettes import Turbo256
+    import pandas as pd
+
+    # Build the before/after tabular data used for plotting
+    before_data: list[dict[str, Any]] = []
+    after_data: list[dict[str, Any]] = []
+
+    if maps:
+        # Ensure feature maps are loaded
+        if self.features_maps is None or len(self.features_maps) == 0:
+            self.load_features()
+
+        fmaps = self.features_maps or []
+
+        if not fmaps:
+            self.logger.error("No feature maps available for plotting.")
+            return
+
+        # Reference (first) sample: use current RT for both before and after
+        ref = fmaps[0]
+        ref_rt = [f.getRT() for f in ref]
+        ref_mz = [f.getMZ() for f in ref]
+        ref_inty = [f.getIntensity() for f in ref]
+        max_ref_inty = max(ref_inty) if ref_inty else 1
+
+        # sample metadata
+        if hasattr(self, 'samples_df') and self.samples_df is not None and not self.samples_df.is_empty():
+            samples_info = self.samples_df.to_pandas()
+            ref_sample_uid = samples_info.iloc[0]['sample_uid'] if 'sample_uid' in samples_info.columns else 'Reference_UID'
+            ref_sample_name = samples_info.iloc[0]['sample_name'] if 'sample_name' in samples_info.columns else 'Reference'
+        else:
+            ref_sample_uid = 'Reference_UID'
+            ref_sample_name = 'Reference'
+
+        for rt, mz, inty in zip(ref_rt, ref_mz, ref_inty):
+            before_data.append({'rt': rt, 'mz': mz, 'inty': inty, 'alpha': inty / max_ref_inty, 'sample_idx': 0, 'sample_name': ref_sample_name, 'sample_uid': ref_sample_uid, 'size': markersize + 2})
+            after_data.append({'rt': rt, 'mz': mz, 'inty': inty, 'alpha': inty / max_ref_inty, 'sample_idx': 0, 'sample_name': ref_sample_name, 'sample_uid': ref_sample_uid, 'size': markersize + 2})
+
+        # Remaining samples
+        for sample_idx, fm in enumerate(fmaps[1:], start=1):
+            mz_vals = []
+            inty_vals = []
+            original_rt = []
+            aligned_rt = []
+
+            for f in fm:
+                try:
+                    orig = f.getMetaValue('original_RT')
+                except Exception:
+                    orig = None
+
+                if orig is None:
+                    original_rt.append(f.getRT())
+                else:
+                    original_rt.append(orig)
+
+                aligned_rt.append(f.getRT())
+                mz_vals.append(f.getMZ())
+                inty_vals.append(f.getIntensity())
+
+            if not inty_vals:
+                continue
+
+            max_inty = max(inty_vals)
+
+            if hasattr(self, 'samples_df') and self.samples_df is not None and not self.samples_df.is_empty():
+                samples_info = self.samples_df.to_pandas()
+                if sample_idx < len(samples_info):
+                    sample_name = samples_info.iloc[sample_idx].get('sample_name', f'Sample {sample_idx}')
+                    sample_uid = samples_info.iloc[sample_idx].get('sample_uid', f'Sample_{sample_idx}_UID')
+                else:
+                    sample_name = f'Sample {sample_idx}'
+                    sample_uid = f'Sample_{sample_idx}_UID'
+            else:
+                sample_name = f'Sample {sample_idx}'
+                sample_uid = f'Sample_{sample_idx}_UID'
 
-    # use alpha value to display feature intensity
-    ax.scatter(
-        [f.getRT() for f in fmaps[0]],
-        [f.getMZ() for f in fmaps[0]],
-        alpha=np.asarray([f.getIntensity() for f in fmaps[0]]) / max([f.getIntensity() for f in fmaps[0]]),
-        s=4,
-    )
+            for rt, mz, inty in zip(original_rt, mz_vals, inty_vals):
+                before_data.append({'rt': rt, 'mz': mz, 'inty': inty, 'alpha': inty / max_inty, 'sample_idx': sample_idx, 'sample_name': sample_name, 'sample_uid': sample_uid, 'size': markersize})
 
-    for fm in fmaps[1:]:
-        ax.scatter(
-            [f.getMetaValue("original_RT") for f in fm],
-            [f.getMZ() for f in fm],
-            alpha=np.asarray([f.getIntensity() for f in fm]) / max([f.getIntensity() for f in fm]),
-            s=2,  # Set symbol size to 3
-        )
+            for rt, mz, inty in zip(aligned_rt, mz_vals, inty_vals):
+                after_data.append({'rt': rt, 'mz': mz, 'inty': inty, 'alpha': inty / max_inty, 'sample_idx': sample_idx, 'sample_name': sample_name, 'sample_uid': sample_uid, 'size': markersize})
 
-    ax = fig.add_subplot(1, 2, 2)
-    ax.set_title("Feature maps after alignment")
-    ax.set_ylabel("m/z")
-    ax.set_xlabel("RT")
-
-    for fm in fmaps:
-        ax.scatter(
-            [f.getRT() for f in fm],
-            [f.getMZ() for f in fm],
-            alpha=np.asarray([f.getIntensity() for f in fm]) / max([f.getIntensity() for f in fm]),
-            s=2,  # Set symbol size to 3
-        )
+    else:
+        # Use features_df
+        if self.features_df is None or self.features_df.is_empty():
+            self.logger.error("No features_df found. Load features first.")
+            return
 
-    fig.tight_layout()
+        required_cols = ['rt', 'mz', 'inty']
+        missing = [c for c in required_cols if c not in self.features_df.columns]
+        if missing:
+            self.logger.error(f"Missing required columns in features_df: {missing}")
+            return
 
+        if 'rt_original' not in self.features_df.columns:
+            self.logger.error("Column 'rt_original' not found in features_df. Alignment may not have been performed.")
+            return
 
-def plot_alignment_bokeh(self, filename=None):
-    from bokeh.plotting import figure, show, output_file
-    from bokeh.layouts import gridplot
+        features_pd = self.features_df.to_pandas()
 
-    feature_maps = self.features_maps
-    ref_index = self.alignment_ref_index
-    if ref_index is None:
-        self.logger.warning("No alignment performed yet.")
-        return
+        sample_col = 'sample_uid' if 'sample_uid' in features_pd.columns else 'sample_name'
+        if sample_col not in features_pd.columns:
+            self.logger.error("No sample identifier column found in features_df.")
+            return
 
-    fmaps = [
-        feature_maps[ref_index],
-        *feature_maps[:ref_index],
-        *feature_maps[ref_index + 1 :],
-    ]
+        samples = features_pd[sample_col].unique()
 
-    # Create Bokeh figures
-    p1 = figure(
-        title="Feature maps before alignment",
-        width=600,
-        height=400,
-    )
-    p1.xaxis.axis_label = "RT"
-    p1.yaxis.axis_label = "m/z"
-    p2 = figure(
-        title="Feature maps after alignment",
-        width=600,
-        height=400,
-    )
-    p2.xaxis.axis_label = "RT"
-    p2.yaxis.axis_label = "m/z"
-
-    # Plot before alignment
-    p1.scatter(
-        x=[f.getRT() for f in fmaps[0]],
-        y=[f.getMZ() for f in fmaps[0]],
-        size=4,
-        alpha=[f.getIntensity() / max([f.getIntensity() for f in fmaps[0]]) for f in fmaps[0]],
-        color="blue",
-    )
+        for sample_idx, sample in enumerate(samples):
+            sample_data = features_pd[features_pd[sample_col] == sample]
+            max_inty = sample_data['inty'].max() if sample_data['inty'].max() > 0 else 1
+            sample_name = str(sample)
+            sample_uid = sample if sample_col == 'sample_uid' else (sample_data['sample_uid'].iloc[0] if 'sample_uid' in sample_data.columns else sample)
 
-    for fm in fmaps[1:]:
-        p1.scatter(
-            x=[f.getMetaValue("original_RT") for f in fm],
-            y=[f.getMZ() for f in fm],
-            size=2,
-            alpha=[f.getIntensity() / max([f.getIntensity() for f in fm]) for f in fm],
-            color="green",
-        )
+            for _, row in sample_data.iterrows():
+                before_data.append({'rt': row['rt_original'], 'mz': row['mz'], 'inty': row['inty'], 'alpha': row['inty'] / max_inty, 'sample_idx': sample_idx, 'sample_name': sample_name, 'sample_uid': sample_uid, 'size': markersize + 2 if sample_idx == 0 else markersize})
+                after_data.append({'rt': row['rt'], 'mz': row['mz'], 'inty': row['inty'], 'alpha': row['inty'] / max_inty, 'sample_idx': sample_idx, 'sample_name': sample_name, 'sample_uid': sample_uid, 'size': markersize + 2 if sample_idx == 0 else markersize})
 
-    # Plot after alignment
-    for fm in fmaps:
-        p2.scatter(
-            x=[f.getRT() for f in fm],
-            y=[f.getMZ() for f in fm],
-            size=2,
-            alpha=[f.getIntensity() / max([f.getIntensity() for f in fm]) for f in fm],
-            color="red",
-        )
+    # Ensure dataframes exist even if empty
+    before_df = pd.DataFrame(before_data)
+    after_df = pd.DataFrame(after_data)
 
-    # Arrange plots in a grid
-    # Link the x_range and y_range of both plots for synchronized zooming/panning
-    p2.x_range = p1.x_range
-    p2.y_range = p1.y_range
+    # Create ColumnDataSources (safe even for empty dfs)
+    from bokeh.models import ColumnDataSource
 
-    grid = gridplot([[p1, p2]])
+    before_source = ColumnDataSource(before_df)
+    after_source = ColumnDataSource(after_df)
 
-    # Output to file and show
+    # Create Bokeh figures
+    p1 = figure(width=width, height=height, title='Original RT', x_axis_label='Retention Time (s)', y_axis_label='m/z', tools='pan,wheel_zoom,box_zoom,reset,save')
+    p1.outline_line_color = None
+    p1.background_fill_color = 'white'
+    p1.border_fill_color = 'white'
+    p1.min_border = 0
+
+    p2 = figure(width=width, height=height, title='Current RT', x_axis_label='Retention Time (s)', y_axis_label='m/z', tools='pan,wheel_zoom,box_zoom,reset,save', x_range=p1.x_range, y_range=p1.y_range)
+    p2.outline_line_color = None
+    p2.background_fill_color = 'white'
+    p2.border_fill_color = 'white'
+    p2.min_border = 0
+
+    # Color mapping using Turbo256
+    unique_samples = sorted(list(set(before_df['sample_idx'].tolist()))) if not before_df.empty else []
+    colors = Turbo256
+    color_map: dict[int, str] = {}
+    n = max(1, len(unique_samples))
+    step = max(1, 256 // n)
+    for i, sample_idx in enumerate(unique_samples):
+        color_map[sample_idx] = colors[(i * step) % 256]
+
+    renderers_before = []
+    renderers_after = []
+
+    for sample_idx in unique_samples:
+        sb = before_df[before_df['sample_idx'] == sample_idx]
+        sa = after_df[after_df['sample_idx'] == sample_idx]
+        color = color_map.get(sample_idx, '#000000')
+
+        if not sb.empty:
+            src = ColumnDataSource(sb)
+            r = p1.scatter('rt', 'mz', size='size', color=color, alpha='alpha', source=src)
+            renderers_before.append(r)
+
+        if not sa.empty:
+            src = ColumnDataSource(sa)
+            r = p2.scatter('rt', 'mz', size='size', color=color, alpha='alpha', source=src)
+            renderers_after.append(r)
+
+    # Add hover tools
+    hover1 = HoverTool(tooltips=[('Sample UID', '@sample_uid'), ('Sample Name', '@sample_name'), ('RT', '@rt{0.00}'), ('m/z', '@mz{0.0000}'), ('Intensity', '@inty{0.0e+0}')], renderers=renderers_before)
+    p1.add_tools(hover1)
+
+    hover2 = HoverTool(tooltips=[('Sample UID', '@sample_uid'), ('Sample Name', '@sample_name'), ('RT', '@rt{0.00}'), ('m/z', '@mz{0.0000}'), ('Intensity', '@inty{0.0e+0}')], renderers=renderers_after)
+    p2.add_tools(hover2)
+
+    # Create layout with both plots side by side
+    # Use the aliased bokeh_row and set sizing_mode, width and height to avoid validation warnings.
+    layout = bokeh_row(p1, p2, sizing_mode='fixed', width=width, height=height)
+
+    # Output and show
     if filename:
+        from bokeh.plotting import output_file, show
         output_file(filename)
-    show(grid)
+        show(layout)
+    else:
+        from bokeh.plotting import show
+        show(layout)
+
+    return layout
 
 
 def plot_consensus_2d(
@@ -163,11 +240,11 @@ def plot_consensus_2d(
     width=900,
     height=900,
     mz_range=None,
-    rt_range=None
+    rt_range=None,
 ):
     """
     Plot consensus features in a 2D scatter plot with retention time vs m/z.
-    
+
     Parameters:
         filename (str, optional): Path to save the plot
         colorby (str): Column name to use for color mapping (default: "number_samples")
@@ -187,13 +264,13 @@ def plot_consensus_2d(
         self.logger.error("No consensus map found.")
         return
     data = self.consensus_df.clone()
-    
+
     # Filter by mz_range and rt_range if provided
     if mz_range is not None:
         data = data.filter((pl.col("mz") >= mz_range[0]) & (pl.col("mz") <= mz_range[1]))
     if rt_range is not None:
         data = data.filter((pl.col("rt") >= rt_range[0]) & (pl.col("rt") <= rt_range[1]))
-    
+
     if colorby not in data.columns:
         self.logger.error(f"Column {colorby} not found in consensus_df.")
         return
@@ -339,16 +416,16 @@ def plot_samples_2d(
     alpha="inty",
     cmap="Turbo256",
     max_features=50000,
-    width=900,
-    height=900,
+    width=600,
+    height=600,
     mz_range=None,
-    rt_range=None
+    rt_range=None,
 ):
     """
     Plot all feature maps for sample_uid in parameter uids in an overlaid scatter plot.
     Each sample is a different color. Alpha scales with intensity.
     OPTIMIZED VERSION: Uses vectorized operations and batch processing.
-    
+
     Parameters:
         samples: Sample UIDs to plot
         filename (str, optional): Path to save the plot
@@ -366,6 +443,12 @@ def plot_samples_2d(
         rt_range (tuple, optional): Retention time range for filtering features (min_rt, max_rt)
     """
 
+    # Local bokeh imports to avoid heavy top-level dependency
+    from bokeh.plotting import figure, show, output_file
+    from bokeh.io.export import export_png
+    from bokeh.models import ColumnDataSource, HoverTool
+    from bokeh.palettes import Turbo256
+
     sample_uids = self._get_sample_uids(samples)
 
     if not sample_uids:
@@ -385,7 +468,7 @@ def plot_samples_2d(
 
     # OPTIMIZATION 1: Batch filter all features for selected samples at once
     features_batch = self.features_df.filter(pl.col("sample_uid").is_in(sample_uids))
-    
+
     # Filter by mz_range and rt_range if provided
     if mz_range is not None:
         features_batch = features_batch.filter((pl.col("mz") >= mz_range[0]) & (pl.col("mz") <= mz_range[1]))
@@ -457,7 +540,10 @@ def plot_samples_2d(
     color_values = {}
     sample_names = {}
 
-    for uid in sample_uids:
+    # Decide whether to show tqdm based on log level (show for INFO/DEBUG/TRACE)
+    tqdm_disable = self.log_level not in ["TRACE", "DEBUG", "INFO"]
+
+    for uid in tqdm(sample_uids, desc="Plotting BPCs", disable=tqdm_disable):
         sample_data = features_pd[features_pd["sample_uid"] == uid]
         if sample_data.empty:
             continue
@@ -527,7 +613,9 @@ def plot_samples_2d(
         p.add_tools(hover)
 
     # Remove legend from plot
-    p.legend.visible = False
+    # Only set legend properties if a legend was actually created to avoid Bokeh warnings
+    if getattr(p, "legend", None) and len(p.legend) > 0:
+        p.legend.visible = False
     if filename:
         if filename.endswith(".html"):
             output_file(filename)
@@ -542,6 +630,441 @@ def plot_samples_2d(
     return
 
 
+def plot_bpc(
+    self,
+    samples=None,
+    title: str | None = None,
+    filename: str | None = None,
+    width: int = 1000,
+    height: int = 300,
+    rt_unit: str = "s",
+    original: bool = False,
+):
+    """
+    Plot Base Peak Chromatograms (BPC) for selected samples overlayed using Bokeh.
+
+    This collects per-sample BPCs via `get_bpc(self, sample=uid)` and overlays them.
+    Colors are mapped per-sample using the same Turbo256 palette as `plot_samples_2d`.
+    Parameters:
+        original (bool): If True, attempt to map RTs back to original RTs using `features_df`.
+                         If False (default), return current/aligned RTs.
+    """
+    # Local imports to avoid heavy top-level deps / circular imports
+    from bokeh.plotting import figure, show, output_file
+    from bokeh.models import ColumnDataSource, HoverTool
+    from bokeh.io.export import export_png
+    from bokeh.palettes import Turbo256
+    from masster.study.helpers import get_bpc
+
+    sample_uids = self._get_sample_uids(samples)
+    if not sample_uids:
+        self.logger.error("No valid sample_uids provided for BPC plotting.")
+        return
+
+    # Debug: show which sample_uids we will process
+    self.logger.debug(f"plot_bpc: sample_uids={sample_uids}")
+
+    colors = Turbo256
+    n = max(1, len(sample_uids))
+    step = max(1, 256 // n)
+    color_map = {uid: colors[(i * step) % 256] for i, uid in enumerate(sample_uids)}
+
+    # If plotting original (uncorrected) RTs, use the requested title.
+    if original:
+        plot_title = "Base Peak Chromatogarms (uncorrected)"
+    else:
+        plot_title = title or "Base Peak Chromatograms"
+
+    p = figure(width=width, height=height, title=plot_title, tools="pan,wheel_zoom,box_zoom,reset,save")
+    p.xaxis.axis_label = f"Retention Time ({rt_unit})"
+    p.yaxis.axis_label = "Intensity"
+
+    renderers = []
+
+    # Build sample name mapping once
+    samples_info = None
+    if hasattr(self, "samples_df") and self.samples_df is not None:
+        try:
+            samples_info = self.samples_df.to_pandas()
+        except Exception:
+            samples_info = None
+
+    for uid in sample_uids:
+        try:
+            chrom = get_bpc(self, sample=uid, rt_unit=rt_unit, label=None, original=original)
+        except Exception as e:
+            # log and skip samples we can't compute BPC for
+            self.logger.debug(f"Skipping sample {uid} for BPC: {e}")
+            continue
+
+        # extract arrays
+        try:
+            # prefer Chromatogram API
+            chrom_dict = chrom.to_dict() if hasattr(chrom, "to_dict") else {"rt": getattr(chrom, "rt"), "inty": getattr(chrom, "inty")}
+            rt = chrom_dict.get("rt")
+            inty = chrom_dict.get("inty")
+        except Exception:
+            try:
+                rt = chrom.rt
+                inty = chrom.inty
+            except Exception as e:
+                self.logger.debug(f"Invalid chromatogram for sample {uid}: {e}")
+                continue
+
+        if rt is None or inty is None:
+            continue
+
+        # Ensure numpy arrays
+        import numpy as _np
+
+        rt = _np.asarray(rt)
+        inty = _np.asarray(inty)
+        if rt.size == 0 or inty.size == 0:
+            continue
+
+        # Sort by rt
+        idx = _np.argsort(rt)
+        rt = rt[idx]
+        inty = inty[idx]
+
+        sample_name = str(uid)
+        if samples_info is not None:
+            try:
+                row = samples_info[samples_info["sample_uid"] == uid]
+                if not row.empty:
+                    sample_name = row.iloc[0].get("sample_name", sample_name)
+            except Exception:
+                pass
+        # Determine color for this sample early so we can log it
+        color = color_map.get(uid, "#000000")
+
+        # Debug: log sample processing details
+        self.logger.debug(
+            f"Processing BPC for sample_uid={uid}, sample_name={sample_name}, rt_len={rt.size}, color={color}"
+        )
+
+        data = {"rt": rt, "inty": inty, "sample": [sample_name] * len(rt)}
+        src = ColumnDataSource(data)
+
+        r_line = p.line("rt", "inty", source=src, line_width=1, color=color, legend_label=str(sample_name))
+        r_points = p.scatter("rt", "inty", source=src, size=2, color=color, alpha=0.6)
+        renderers.append(r_line)
+
+    if not renderers:
+        self.logger.warning("No BPC curves to plot for the selected samples.")
+        return
+
+    hover = HoverTool(tooltips=[("sample", "@sample"), ("rt", "@rt{0.00}"), ("inty", "@inty{0.0e+0}")], renderers=renderers)
+    p.add_tools(hover)
+
+    # Only set legend properties if a legend was actually created to avoid Bokeh warnings
+    if getattr(p, "legend", None) and len(p.legend) > 0:
+        p.legend.visible = False
+
+    if filename:
+        if filename.endswith(".html"):
+            output_file(filename)
+            show(p)
+        elif filename.endswith(".png"):
+            try:
+                export_png(p, filename=filename)
+            except Exception:
+                # fallback to saving HTML
+                output_file(filename.replace(".png", ".html"))
+                show(p)
+        else:
+            output_file(filename)
+            show(p)
+    else:
+        show(p)
+
+    return p
+
+
+def plot_eic(
+    self,
+    mz,
+    mz_tol=0.01,
+    samples=None,
+    title: str | None = None,
+    filename: str | None = None,
+    width: int = 1000,
+    height: int = 300,
+    rt_unit: str = "s",
+    original: bool = False,
+):
+    """
+    Plot Extracted Ion Chromatograms (EIC) for a target m/z (± mz_tol) for selected samples.
+
+    Parameters mirror `plot_bpc` with additional `mz` and `mz_tol` arguments. The function
+    retrieves a Sample object for each sample UID, calls `sample.get_eic(mz, mz_tol)`, and
+    overlays the resulting chromatograms.
+    """
+    # Local imports to avoid heavy top-level deps / circular imports
+    from bokeh.plotting import figure, show, output_file
+    from bokeh.models import ColumnDataSource, HoverTool
+    from bokeh.io.export import export_png
+    from bokeh.palettes import Turbo256
+    from masster.study.helpers import get_eic
+
+    if mz is None:
+        self.logger.error("mz must be provided for EIC plotting")
+        return
+
+    sample_uids = self._get_sample_uids(samples)
+    if not sample_uids:
+        self.logger.error("No valid sample_uids provided for EIC plotting.")
+        return
+
+    colors = Turbo256
+    n = max(1, len(sample_uids))
+    step = max(1, 256 // n)
+    color_map = {uid: colors[(i * step) % 256] for i, uid in enumerate(sample_uids)}
+
+    plot_title = title or f"Extracted Ion Chromatograms (m/z={mz:.4f} ± {mz_tol})"
+
+    p = figure(width=width, height=height, title=plot_title, tools="pan,wheel_zoom,box_zoom,reset,save")
+    p.xaxis.axis_label = f"Retention Time ({rt_unit})"
+    p.yaxis.axis_label = "Intensity"
+
+    renderers = []
+
+    # Build sample name mapping once
+    samples_info = None
+    if hasattr(self, "samples_df") and self.samples_df is not None:
+        try:
+            samples_info = self.samples_df.to_pandas()
+        except Exception:
+            samples_info = None
+
+    for uid in sample_uids:
+        try:
+            chrom = get_eic(self, sample=uid, mz=mz, mz_tol=mz_tol, rt_unit=rt_unit, label=None)
+        except Exception as e:
+            # log and skip samples we can't compute EIC for
+            self.logger.debug(f"Skipping sample {uid} for EIC: {e}")
+            continue
+
+        # extract arrays
+        try:
+            # prefer Chromatogram API
+            chrom_dict = chrom.to_dict() if hasattr(chrom, "to_dict") else {"rt": getattr(chrom, "rt"), "inty": getattr(chrom, "inty")}
+            rt = chrom_dict.get("rt")
+            inty = chrom_dict.get("inty")
+        except Exception:
+            try:
+                rt = chrom.rt
+                inty = chrom.inty
+            except Exception as e:
+                self.logger.debug(f"Invalid chromatogram for sample {uid}: {e}")
+                continue
+
+        if rt is None or inty is None:
+            continue
+
+        import numpy as _np
+
+        rt = _np.asarray(rt)
+        inty = _np.asarray(inty)
+        if rt.size == 0 or inty.size == 0:
+            continue
+
+        # Sort by rt
+        idx = _np.argsort(rt)
+        rt = rt[idx]
+        inty = inty[idx]
+
+        sample_name = str(uid)
+        if samples_info is not None:
+            try:
+                row = samples_info[samples_info["sample_uid"] == uid]
+                if not row.empty:
+                    sample_name = row.iloc[0].get("sample_name", sample_name)
+            except Exception:
+                pass
+
+        color = color_map.get(uid, "#000000")
+
+        data = {"rt": rt, "inty": inty, "sample": [sample_name] * len(rt)}
+        src = ColumnDataSource(data)
+
+        r_line = p.line("rt", "inty", source=src, line_width=1, color=color, legend_label=str(sample_name))
+        p.scatter("rt", "inty", source=src, size=2, color=color, alpha=0.6)
+        renderers.append(r_line)
+
+    if not renderers:
+        self.logger.warning("No EIC curves to plot for the selected samples.")
+        return
+
+    hover = HoverTool(tooltips=[("sample", "@sample"), ("rt", "@rt{0.00}"), ("inty", "@inty{0.0e+0}")], renderers=renderers)
+    p.add_tools(hover)
+
+    if getattr(p, "legend", None) and len(p.legend) > 0:
+        p.legend.visible = False
+
+    if filename:
+        if filename.endswith(".html"):
+            output_file(filename)
+            show(p)
+        elif filename.endswith(".png"):
+            try:
+                export_png(p, filename=filename)
+            except Exception:
+                output_file(filename.replace(".png", ".html"))
+                show(p)
+        else:
+            output_file(filename)
+            show(p)
+    else:
+        show(p)
+
+    return p
+
+
+def plot_rt_correction(
+    self,
+    samples=None,
+    title: str | None = None,
+    filename: str | None = None,
+    width: int = 1000,
+    height: int = 300,
+    rt_unit: str = "s",
+):
+    """
+    Plot RT correction per sample: (rt - rt_original) vs rt overlayed for selected samples.
+
+    This uses the same color mapping as `plot_bpc` so curves for the same samples match.
+    """
+    from bokeh.plotting import figure, show, output_file
+    from bokeh.models import ColumnDataSource, HoverTool
+    from bokeh.palettes import Turbo256
+    import numpy as _np
+
+    # Validate features dataframe
+    if self.features_df is None or self.features_df.is_empty():
+        self.logger.error("No features_df found. Load features first.")
+        return
+
+    if "rt_original" not in self.features_df.columns:
+        self.logger.error("Column 'rt_original' not found in features_df. Alignment/backup RTs missing.")
+        return
+
+    sample_uids = self._get_sample_uids(samples)
+    if not sample_uids:
+        self.logger.error("No valid sample_uids provided for RT correction plotting.")
+        return
+
+    # Color mapping like plot_bpc
+    colors = Turbo256
+    n = max(1, len(sample_uids))
+    step = max(1, 256 // n)
+    color_map = {uid: colors[(i * step) % 256] for i, uid in enumerate(sample_uids)}
+
+    p = figure(width=width, height=height, title=title or "RT correction", tools="pan,wheel_zoom,box_zoom,reset,save")
+    p.xaxis.axis_label = f"Retention Time ({rt_unit})"
+    p.yaxis.axis_label = "RT - RT_original (s)"
+
+    samples_info = None
+    if hasattr(self, "samples_df") and self.samples_df is not None:
+        try:
+            samples_info = self.samples_df.to_pandas()
+        except Exception:
+            samples_info = None
+
+    renderers = []
+
+    # Iterate samples and build curves
+    for uid in sample_uids:
+        # Select features belonging to this sample
+        try:
+            if "sample_uid" in self.features_df.columns:
+                sample_feats = self.features_df.filter(pl.col("sample_uid") == uid)
+            elif "sample_name" in self.features_df.columns:
+                sample_feats = self.features_df.filter(pl.col("sample_name") == uid)
+            else:
+                self.logger.debug("No sample identifier column in features_df; skipping sample filtering")
+                continue
+        except Exception as e:
+            self.logger.debug(f"Error filtering features for sample {uid}: {e}")
+            continue
+
+        if sample_feats.is_empty():
+            continue
+
+        # Convert to pandas for easy numeric handling
+        try:
+            df = sample_feats.to_pandas()
+        except Exception:
+            continue
+
+        # Need both rt and rt_original
+        if "rt" not in df.columns or "rt_original" not in df.columns:
+            continue
+
+        # Drop NA and ensure numeric arrays
+        df = df.dropna(subset=["rt", "rt_original"]).copy()
+        if df.empty:
+            continue
+
+        rt = _np.asarray(df["rt"], dtype=float)
+        rt_orig = _np.asarray(df["rt_original"], dtype=float)
+        delta = rt - rt_orig
+
+        # sort by rt
+        idx = _np.argsort(rt)
+        rt = rt[idx]
+        delta = delta[idx]
+
+        sample_name = str(uid)
+        if samples_info is not None:
+            try:
+                row = samples_info[samples_info["sample_uid"] == uid]
+                if not row.empty:
+                    sample_name = row.iloc[0].get("sample_name", sample_name)
+            except Exception:
+                pass
+
+        color = color_map.get(uid, "#000000")
+
+        data = {"rt": rt, "delta": delta, "sample": [sample_name] * len(rt)}
+        src = ColumnDataSource(data)
+
+        r_line = p.line("rt", "delta", source=src, line_width=1, color=color)
+        p.scatter("rt", "delta", source=src, size=2, color=color, alpha=0.6)
+        renderers.append(r_line)
+
+    if not renderers:
+        self.logger.warning("No RT correction curves to plot for the selected samples.")
+        return
+
+    hover = HoverTool(tooltips=[("sample", "@sample"), ("rt", "@rt{0.00}"), ("rt - rt_original", "@delta{0.00}")], renderers=renderers)
+    p.add_tools(hover)
+
+    # Only set legend properties if a legend was actually created to avoid Bokeh warnings
+    if getattr(p, "legend", None) and len(p.legend) > 0:
+        p.legend.visible = False
+
+    if filename:
+        if filename.endswith(".html"):
+            output_file(filename)
+            show(p)
+        elif filename.endswith(".png"):
+            try:
+                from bokeh.io.export import export_png
+
+                export_png(p, filename=filename)
+            except Exception:
+                output_file(filename.replace(".png", ".html"))
+                show(p)
+        else:
+            output_file(filename)
+            show(p)
+    else:
+        show(p)
+
+    return p
+
+
 def plot_chrom(
     self,
     uids=None,
@@ -560,6 +1083,9 @@ def plot_chrom(
         self.logger.error("No chromatogram data found.")
         return
 
+    # Local import for color palette
+    from bokeh.palettes import Turbo256
+
     # Assign a fixed color to each sample/column
     sample_names = [col for col in chroms.columns if col not in ["consensus_uid"]]
     if not sample_names:
@@ -569,12 +1095,12 @@ def plot_chrom(
 
     plots = []
     self.logger.info(f"Plotting {chroms.shape[0]} chromatograms...")
-    tdqm_disable = self.log_level not in ["TRACE", "DEBUG", "INFO"]
+    tqdm_disable = self.log_level not in ["TRACE", "DEBUG", "INFO"]
     for row in tqdm(
         chroms.iter_rows(named=True),
         total=chroms.shape[0],
         desc=f"{datetime.now().strftime('%Y-%m-%d %H:%M:%S.%f')[:-3]} | INFO     | {self.log_label}Plot chromatograms",
-        disable=tdqm_disable,
+        disable=tqdm_disable,
     ):
         consensus_uid = row["consensus_uid"]  # Get consensus_uid from the row
         consensus_id = consensus_uid  # Use the same value for consensus_id
@@ -698,3 +1224,592 @@ def plot_chrom(
         # In a server context, return the panel object instead of showing or saving directly
         # return panel.panel(layout)
         panel.panel(layout).show()
+
+
+def plot_consensus_stats(
+    self,
+    filename=None,
+    width=1200,
+    height=1200,
+    alpha=0.6,
+    markersize=3,
+):
+    """
+    Plot a scatter plot matrix (SPLOM) of consensus statistics using Bokeh.
+
+    Parameters:
+        filename (str, optional): Output filename for saving the plot
+        width (int): Overall width of the plot (default: 1200)
+        height (int): Overall height of the plot (default: 1200)
+        alpha (float): Point transparency (default: 0.6)
+        markersize (int): Size of points (default: 5)
+    """
+    from bokeh.layouts import gridplot
+    from bokeh.models import ColumnDataSource, HoverTool
+    from bokeh.plotting import figure, show, output_file
+
+    # Check if consensus_df exists and has data
+    if self.consensus_df is None or self.consensus_df.is_empty():
+        self.logger.error("No consensus data available. Run merge/find_consensus first.")
+        return
+
+    # Define the columns to plot
+    columns = [
+        "rt",
+        "mz",
+        "number_samples",
+        "log10_quality",
+        "mz_delta_mean",
+        "rt_delta_mean",
+        "chrom_coherence_mean",
+        "chrom_prominence_scaled_mean",
+        "inty_mean",
+        "number_ms2",
+    ]
+
+    # Check which columns exist in the dataframe and compute missing ones
+    available_columns = self.consensus_df.columns
+    data_df = self.consensus_df.clone()
+
+    # Add log10_quality if quality exists
+    if "quality" in available_columns and "log10_quality" not in available_columns:
+        data_df = data_df.with_columns(
+            pl.col("quality").log10().alias("log10_quality"),
+        )
+
+    # Filter columns that actually exist
+    final_columns = [col for col in columns if col in data_df.columns]
+
+    if len(final_columns) < 2:
+        self.logger.error(f"Need at least 2 columns for SPLOM. Available: {final_columns}")
+        return
+
+    self.logger.debug(f"Creating SPLOM with columns: {final_columns}")
+
+    # Add important ID columns for tooltips even if not plotting them
+    tooltip_columns = []
+    for id_col in ["consensus_uid", "consensus_id"]:
+        if id_col in data_df.columns and id_col not in final_columns:
+            tooltip_columns.append(id_col)
+
+    # Select plotting columns plus tooltip columns
+    all_columns = final_columns + tooltip_columns
+    data_pd = data_df.select(all_columns).to_pandas()
+
+    # Remove any infinite or NaN values
+    data_pd = data_pd.replace([np.inf, -np.inf], np.nan).dropna()
+
+    if data_pd.empty:
+        self.logger.error("No valid data after removing NaN/infinite values.")
+        return
+
+    source = ColumnDataSource(data_pd)
+
+    n_vars = len(final_columns)
+
+    # Fixed dimensions - override user input to ensure consistent layout
+    total_width = 1200
+    total_height = 1200
+
+    # Calculate plot sizes to ensure uniform inner plot areas
+    # First column needs extra width for y-axis labels
+    plot_width_first = 180  # Wider to account for y-axis labels
+    plot_width_others = 120  # Standard width for other columns
+    plot_height_normal = 120  # Standard height
+    plot_height_last = 155  # Taller last row to accommodate x-axis labels while keeping inner plot area same size
+
+    # Create grid of plots with variable outer sizes but equal inner areas
+    plots = []
+
+    for i, y_var in enumerate(final_columns):
+        row = []
+        for j, x_var in enumerate(final_columns):
+            # Determine if this plot needs axis labels
+            has_x_label = i == n_vars - 1  # bottom row
+            has_y_label = j == 0  # left column
+
+            # First column wider to accommodate y-axis labels, ensuring equal inner plot areas
+            current_width = plot_width_first if has_y_label else plot_width_others
+            current_height = plot_height_last if has_x_label else plot_height_normal
+
+            p = figure(
+                width=current_width,
+                height=current_height,
+                title=None,  # No title on any plot
+                toolbar_location=None,
+                # Adjusted borders - first column has more space, others minimal
+                min_border_left=70 if has_y_label else 15,
+                min_border_bottom=50 if has_x_label else 15,
+                min_border_right=15,
+                min_border_top=15,
+            )
+
+            # Ensure subplot background and border are explicitly white so the plot looks
+            # correct in dark and light themes.
+            p.outline_line_color = None
+            p.border_fill_color = "white"
+            p.border_fill_alpha = 1.0
+            p.background_fill_color = "white"
+
+            # Remove axis lines to eliminate black lines between plots
+            p.xaxis.axis_line_color = None
+            p.yaxis.axis_line_color = None
+
+            # Keep subtle grid lines for data reference
+            p.grid.visible = True
+            p.grid.grid_line_color = "#E0E0E0"  # Light gray grid lines
+
+            # Set axis labels and formatting
+            if has_x_label:  # bottom row
+                p.xaxis.axis_label = x_var
+                p.xaxis.axis_label_text_font_size = "12pt"
+                p.xaxis.major_label_text_font_size = "9pt"
+                p.xaxis.axis_label_standoff = 15
+            else:
+                p.xaxis.major_label_text_font_size = "0pt"
+                p.xaxis.minor_tick_line_color = None
+                p.xaxis.major_tick_line_color = None
+
+            if has_y_label:  # left column
+                p.yaxis.axis_label = y_var
+                p.yaxis.axis_label_text_font_size = "10pt"  # Smaller y-axis title
+                p.yaxis.major_label_text_font_size = "8pt"
+                p.yaxis.axis_label_standoff = 12
+            else:
+                p.yaxis.major_label_text_font_size = "0pt"
+                p.yaxis.minor_tick_line_color = None
+                p.yaxis.major_tick_line_color = None
+
+            if i == j:
+                # Diagonal: histogram
+                hist, edges = np.histogram(data_pd[x_var], bins=30)
+                p.quad(
+                    top=hist,
+                    bottom=0,
+                    left=edges[:-1],
+                    right=edges[1:],
+                    fill_color="green",
+                    line_color="white",
+                    alpha=alpha,
+                )
+            else:
+                # Off-diagonal: scatter plot
+                scatter = p.scatter(
+                    x=x_var,
+                    y=y_var,
+                    size=markersize,
+                    alpha=alpha,
+                    color="blue",
+                    source=source,
+                )
+
+                # Add hover tool
+                hover = HoverTool(
+                    tooltips=[
+                        (x_var, f"@{x_var}{{0.0000}}"),
+                        (y_var, f"@{y_var}{{0.0000}}"),
+                        (
+                            "consensus_uid",
+                            "@consensus_uid"
+                            if "consensus_uid" in data_pd.columns
+                            else "@consensus_id"
+                            if "consensus_id" in data_pd.columns
+                            else "N/A",
+                        ),
+                        ("rt", "@rt{0.00}" if "rt" in data_pd.columns else "N/A"),
+                        ("mz", "@mz{0.0000}" if "mz" in data_pd.columns else "N/A"),
+                    ],
+                    renderers=[scatter],
+                )
+                p.add_tools(hover)
+
+            row.append(p)
+        plots.append(row)
+
+    # Link axes for same variables
+    for i in range(n_vars):
+        for j in range(n_vars):
+            if i != j:  # Don't link diagonal plots
+                # Link x-axis to other plots in same column
+                for k in range(n_vars):
+                    if k != i and k != j:
+                        plots[i][j].x_range = plots[k][j].x_range
+
+                # Link y-axis to other plots in same row
+                for k in range(n_vars):
+                    if k != j and k != i:
+                        plots[i][j].y_range = plots[i][k].y_range
+
+    # Create grid layout and force overall background/border to white so the outer
+    # container doesn't show dark UI colors in night mode.
+    grid = gridplot(plots)
+
+    # Set overall background and border to white when supported
+    if hasattr(grid, "background_fill_color"):
+        grid.background_fill_color = "white"
+    if hasattr(grid, "border_fill_color"):
+        grid.border_fill_color = "white"
+
+    # Output and show
+    if filename:
+        output_file(filename)
+
+    show(grid)
+    return grid
+
+
+def plot_pca(
+    self,
+    filename=None,
+    width=400,
+    height=400,
+    alpha=0.8,
+    markersize=6,
+    n_components=2,
+    color_by=None,
+    title="PCA of Consensus Matrix",
+):
+    """
+    Plot PCA (Principal Component Analysis) of the consensus matrix using Bokeh.
+
+    Parameters:
+        filename (str, optional): Output filename for saving the plot
+        width (int): Plot width (default: 800)
+        height (int): Plot height (default: 600)
+        alpha (float): Point transparency (default: 0.8)
+        markersize (int): Size of points (default: 8)
+        n_components (int): Number of PCA components to compute (default: 2)
+        color_by (str, optional): Column from samples_df to color points by
+        title (str): Plot title (default: "PCA of Consensus Matrix")
+    """
+    from bokeh.models import ColumnDataSource, HoverTool, ColorBar, LinearColorMapper
+    from bokeh.plotting import figure, show, output_file
+    from bokeh.palettes import Category20, viridis, Turbo256
+    from bokeh.transform import factor_cmap
+    from sklearn.decomposition import PCA
+    from sklearn.preprocessing import StandardScaler
+    import pandas as pd
+    import numpy as np
+
+    # Check if consensus matrix and samples_df exist
+    try:
+        consensus_matrix = self.get_consensus_matrix()
+        samples_df = self.samples_df
+    except Exception as e:
+        self.logger.error(f"Error getting consensus matrix or samples_df: {e}")
+        return
+
+    if consensus_matrix is None or consensus_matrix.shape[0] == 0:
+        self.logger.error("No consensus matrix available. Run merge/find_consensus first.")
+        return
+
+    if samples_df is None or samples_df.is_empty():
+        self.logger.error("No samples dataframe available.")
+        return
+
+    self.logger.info(f"Performing PCA on consensus matrix with shape: {consensus_matrix.shape}")
+
+    # Convert consensus matrix to numpy if it's not already
+    if hasattr(consensus_matrix, "values"):
+        matrix_data = consensus_matrix.values
+    elif hasattr(consensus_matrix, "to_numpy"):
+        matrix_data = consensus_matrix.to_numpy()
+    else:
+        matrix_data = np.array(consensus_matrix)
+
+    # Transpose matrix so samples are rows and features are columns
+    matrix_data = matrix_data.T
+
+    # Handle missing values by replacing with 0
+    matrix_data = np.nan_to_num(matrix_data, nan=0.0, posinf=0.0, neginf=0.0)
+
+    # Standardize the data
+    scaler = StandardScaler()
+    matrix_scaled = scaler.fit_transform(matrix_data)
+
+    # Perform PCA
+    pca = PCA(n_components=n_components)
+    pca_result = pca.fit_transform(matrix_scaled)
+
+    # Get explained variance ratios
+    explained_var = pca.explained_variance_ratio_
+
+    self.logger.info(f"PCA explained variance ratios: {explained_var}")
+
+    # Convert samples_df to pandas for easier manipulation
+    samples_pd = samples_df.to_pandas()
+
+    # Create dataframe with PCA results and sample information
+    pca_df = pd.DataFrame({
+        "PC1": pca_result[:, 0],
+        "PC2": pca_result[:, 1] if n_components > 1 else np.zeros(len(pca_result)),
+    })
+
+    # Add sample information to PCA dataframe
+    if len(samples_pd) == len(pca_df):
+        for col in samples_pd.columns:
+            pca_df[col] = samples_pd[col].values
+    else:
+        self.logger.warning(
+            f"Sample count mismatch: samples_df has {len(samples_pd)} rows, "
+            f"but consensus matrix has {len(pca_df)} samples"
+        )
+
+    # Prepare color mapping
+    color_column = None
+    color_mapper = None
+
+    if color_by and color_by in pca_df.columns:
+        color_column = color_by
+        unique_values = pca_df[color_by].unique()
+
+        # Handle categorical vs numeric coloring
+        if pca_df[color_by].dtype in ["object", "string", "category"]:
+            # Categorical coloring
+            if len(unique_values) <= 20:
+                palette = Category20[min(20, max(3, len(unique_values)))]
+            else:
+                palette = viridis(min(256, len(unique_values)))
+            color_mapper = factor_cmap(color_by, palette, unique_values)
+        else:
+            # Numeric coloring
+            palette = viridis(256)
+            color_mapper = LinearColorMapper(
+                palette=palette,
+                low=pca_df[color_by].min(),
+                high=pca_df[color_by].max(),
+            )
+
+    # Create Bokeh plot
+    p = figure(
+        width=width,
+        height=height,
+        title=f"{title} (PC1: {explained_var[0]:.1%}, PC2: {explained_var[1]:.1%})",
+        tools="pan,wheel_zoom,box_zoom,reset,save",
+    )
+
+    p.xaxis.axis_label = f"PC1 ({explained_var[0]:.1%} variance)"
+    p.yaxis.axis_label = f"PC2 ({explained_var[1]:.1%} variance)"
+
+    # Create data source
+    source = ColumnDataSource(pca_df)
+
+    # Create scatter plot
+    if color_mapper:
+        if isinstance(color_mapper, LinearColorMapper):
+            scatter = p.scatter(
+                "PC1",
+                "PC2",
+                size=markersize,
+                alpha=alpha,
+                color={"field": color_by, "transform": color_mapper},
+                source=source,
+            )
+            # Add colorbar for numeric coloring
+            color_bar = ColorBar(color_mapper=color_mapper, width=8, location=(0, 0))
+            p.add_layout(color_bar, "right")
+        else:
+            scatter = p.scatter(
+                "PC1",
+                "PC2",
+                size=markersize,
+                alpha=alpha,
+                color=color_mapper,
+                source=source,
+                legend_field=color_by,
+            )
+    else:
+        # If no color_by provided, color points by sample similar to plot_samples_2d
+        if "sample_uid" in pca_df.columns or "sample_name" in pca_df.columns:
+            # Choose the identifier to map colors by
+            id_col = "sample_uid" if "sample_uid" in pca_df.columns else "sample_name"
+            sample_ids = list(pd.unique(pca_df[id_col]))
+            colors = Turbo256
+            color_map = {uid: colors[i * (256 // max(1, len(sample_ids)))] for i, uid in enumerate(sample_ids)}
+            # Map colors into dataframe
+            pca_df["color"] = [color_map[x] for x in pca_df[id_col]]
+            # Update the ColumnDataSource with new color column
+            source = ColumnDataSource(pca_df)
+            scatter = p.scatter(
+                "PC1",
+                "PC2",
+                size=markersize,
+                alpha=alpha,
+                color="color",
+                source=source,
+            )
+        else:
+            scatter = p.scatter(
+                "PC1",
+                "PC2",
+                size=markersize,
+                alpha=alpha,
+                color="blue",
+                source=source,
+            )
+
+    # Create comprehensive hover tooltips with all sample information
+    tooltip_list = []
+
+    # Columns to exclude from tooltips (file paths and internal/plot fields)
+    excluded_cols = {"file_source", "file_path", "sample_path", "map_id", "PC1", "PC2", "ms1", "ms2"}
+
+    # Add all sample dataframe columns to tooltips, skipping excluded ones
+    for col in samples_pd.columns:
+        if col in excluded_cols:
+            continue
+        if col in pca_df.columns:
+            if pca_df[col].dtype in ["float64", "float32"]:
+                tooltip_list.append((col, f"@{col}{{0.00}}"))
+            else:
+                tooltip_list.append((col, f"@{col}"))
+
+    hover = HoverTool(
+        tooltips=tooltip_list,
+        renderers=[scatter],
+    )
+    p.add_tools(hover)
+
+    # Add legend if using categorical coloring
+    if color_mapper and not isinstance(color_mapper, LinearColorMapper) and color_by:
+        # Only set legend properties if legends exist (avoid Bokeh warning when none created)
+        if getattr(p, "legend", None) and len(p.legend) > 0:
+            p.legend.location = "top_left"
+            p.legend.click_policy = "hide"
+
+    # Output and show
+    if filename:
+        output_file(filename)
+
+    show(p)
+    return p
+
+def plot_tic(
+    self,
+    samples=None,
+    title: str | None = None,
+    filename: str | None = None,
+    width: int = 1000,
+    height: int = 300,
+    rt_unit: str = "s",
+    original: bool = False,
+):
+    """
+    Plot Total Ion Chromatograms (TIC) for selected samples overlayed using Bokeh.
+
+    Parameters and behavior mirror `plot_bpc` but use per-sample TICs (get_tic).
+    """
+    # Local imports to avoid heavy top-level deps / circular imports
+    from bokeh.plotting import figure, show, output_file
+    from bokeh.models import ColumnDataSource, HoverTool
+    from bokeh.io.export import export_png
+    from bokeh.palettes import Turbo256
+    from masster.study.helpers import get_tic
+
+    sample_uids = self._get_sample_uids(samples)
+    if not sample_uids:
+        self.logger.error("No valid sample_uids provided for TIC plotting.")
+        return
+
+    colors = Turbo256
+    n = max(1, len(sample_uids))
+    step = max(1, 256 // n)
+    color_map = {uid: colors[(i * step) % 256] for i, uid in enumerate(sample_uids)}
+
+    plot_title = title or "Total Ion Chromatograms"
+
+    p = figure(width=width, height=height, title=plot_title, tools="pan,wheel_zoom,box_zoom,reset,save")
+    p.xaxis.axis_label = f"Retention Time ({rt_unit})"
+    p.yaxis.axis_label = "Intensity"
+
+    renderers = []
+
+    # Build sample name mapping once
+    samples_info = None
+    if hasattr(self, "samples_df") and self.samples_df is not None:
+        try:
+            samples_info = self.samples_df.to_pandas()
+        except Exception:
+            samples_info = None
+
+    for uid in sample_uids:
+        try:
+            chrom = get_tic(self, sample=uid, label=None)
+        except Exception as e:
+            self.logger.debug(f"Skipping sample {uid} for TIC: {e}")
+            continue
+
+        # extract arrays
+        try:
+            chrom_dict = chrom.to_dict() if hasattr(chrom, "to_dict") else {"rt": getattr(chrom, "rt"), "inty": getattr(chrom, "inty")}
+            rt = chrom_dict.get("rt")
+            inty = chrom_dict.get("inty")
+        except Exception:
+            try:
+                rt = chrom.rt
+                inty = chrom.inty
+            except Exception as e:
+                self.logger.debug(f"Invalid chromatogram for sample {uid}: {e}")
+                continue
+
+        if rt is None or inty is None:
+            continue
+
+        import numpy as _np
+
+        rt = _np.asarray(rt)
+        inty = _np.asarray(inty)
+        if rt.size == 0 or inty.size == 0:
+            continue
+
+        # Sort by rt
+        idx = _np.argsort(rt)
+        rt = rt[idx]
+        inty = inty[idx]
+
+        sample_name = str(uid)
+        if samples_info is not None:
+            try:
+                row = samples_info[samples_info["sample_uid"] == uid]
+                if not row.empty:
+                    sample_name = row.iloc[0].get("sample_name", sample_name)
+            except Exception:
+                pass
+
+        color = color_map.get(uid, "#000000")
+
+        data = {"rt": rt, "inty": inty, "sample": [sample_name] * len(rt)}
+        src = ColumnDataSource(data)
+
+        r_line = p.line("rt", "inty", source=src, line_width=1, color=color, legend_label=str(sample_name))
+        p.scatter("rt", "inty", source=src, size=2, color=color, alpha=0.6)
+        renderers.append(r_line)
+
+    if not renderers:
+        self.logger.warning("No TIC curves to plot for the selected samples.")
+        return
+
+    hover = HoverTool(tooltips=[("sample", "@sample"), ("rt", "@rt{0.00}"), ("inty", "@inty{0.0e+0}")], renderers=renderers)
+    p.add_tools(hover)
+
+    # Only set legend properties if a legend was actually created to avoid Bokeh warnings
+    if getattr(p, "legend", None) and len(p.legend) > 0:
+        p.legend.visible = False
+
+    if filename:
+        if filename.endswith(".html"):
+            output_file(filename)
+            show(p)
+        elif filename.endswith(".png"):
+            try:
+                export_png(p, filename=filename)
+            except Exception:
+                output_file(filename.replace(".png", ".html"))
+                show(p)
+        else:
+            output_file(filename)
+            show(p)
+    else:
+        show(p)
+
+    return p