diff --git a/pyopenms_viz/_bokeh/core.py b/pyopenms_viz/_bokeh/core.py
index 0450d71f..958ee05a 100644
--- a/pyopenms_viz/_bokeh/core.py
+++ b/pyopenms_viz/_bokeh/core.py
@@ -545,7 +545,11 @@ class BOKEHSpectrumPlot(BOKEH_MSPlot, SpectrumPlot):
Class for assembling a Bokeh spectrum plot
"""
- pass
+ def plot_peptide_sequence(self, peptide_sequence: str, matched_fragments=None):
+ """
+ Raises a NotImplementedError because peptide sequence plotting is not supported for Bokeh.
+ """
+ raise NotImplementedError("Peptide sequence plotting is currently unsupported in the Bokeh backend.")
class BOKEHPeakMapPlot(BOKEH_MSPlot, PeakMapPlot):
diff --git a/pyopenms_viz/_config.py b/pyopenms_viz/_config.py
index 0b79487c..d1e78136 100644
--- a/pyopenms_viz/_config.py
+++ b/pyopenms_viz/_config.py
@@ -362,6 +362,12 @@ class SpectrumConfig(VLineConfig):
mirror_spectrum: bool = False
peak_color: str | None = None
+ # New fields for peptide sequence plotting
+ display_peptide_sequence: bool = False
+ peptide_sequence: str = ""
+ matched_fragments: list[tuple] = field(default_factory=list)
+
+
# Binning settings
bin_peaks: Union[Literal["auto"], bool] = False
bin_method: Literal["none", "sturges", "freedman-diaconis", "mz-tol-bin"] = (
diff --git a/pyopenms_viz/_core.py b/pyopenms_viz/_core.py
index 62d51c02..0f73064b 100644
--- a/pyopenms_viz/_core.py
+++ b/pyopenms_viz/_core.py
@@ -688,6 +688,14 @@ def __init__(
super().__init__(data, **kwargs)
self.plot()
+
+ @abstractmethod
+ def plot_peptide_sequence(self, peptide_sequence: str, matched_fragments=None):
+ """
+ Renders a peptide sequence annotation on the spectrum.
+ Must be implemented by each backend (e.g., matplotlib).
+ """
+ pass
def load_config(self, **kwargs):
if self._config is None:
@@ -796,6 +804,13 @@ def plot(self):
self.canvas, ann_texts, ann_xs, ann_ys, ann_colors
)
+ # If config says display_sequence, call the abstract method
+ if self.display_peptide_sequence and self.peptide_sequence:
+ self.plot_peptide_sequence(
+ self.peptide_sequence,
+ matched_fragments=self.matched_fragments
+ )
+
# Mirror spectrum
if self.mirror_spectrum and self.reference_spectrum is not None:
## create a mirror spectrum
diff --git a/pyopenms_viz/_matplotlib/core.py b/pyopenms_viz/_matplotlib/core.py
index 11e7c737..928e1f94 100644
--- a/pyopenms_viz/_matplotlib/core.py
+++ b/pyopenms_viz/_matplotlib/core.py
@@ -583,7 +583,102 @@ class MATPLOTLIBSpectrumPlot(MATPLOTLIB_MSPlot, SpectrumPlot):
Class for assembling a matplotlib spectrum plot
"""
- pass
+ def plot_peptide_sequence(
+ self,
+ peptide_sequence: str,
+ matched_fragments=None,
+ x: float = 0.5, # center horizontal position (axes fraction)
+ y: float = 0.95, # vertical position (axes fraction)
+ spacing: float = 0.05, # spacing between residues (axes fraction)
+ fontsize: int = 12,
+ fontsize_frag: int = 10,
+ frag_len: float = 0.05 # length for fragment lines (in axes fraction)
+ ):
+ """
+ Plot peptide sequence with matched fragments indicated.
+
+ The peptide is displayed in the top corner and the fragmentation pattern
+ is drawn as lines coming out from the letters -- using the dataframe columns
+ 'ion_annotation' and 'ion_color' (or 'color_annotation'). No extra arguments are needed.
+ """
+ ax = self.ax
+
+ # Compute starting x so that the sequence is centered at x.
+ n_residues = len(peptide_sequence)
+ start_x = x - n_residues * spacing / 2 + spacing / 2
+
+ # Draw each amino acid letter.
+ for i, aa in enumerate(peptide_sequence):
+ ax.text(
+ start_x + i * spacing,
+ y,
+ aa,
+ fontsize=fontsize,
+ ha="center",
+ va="center",
+ transform=ax.transAxes,
+ )
+
+ # If matched_fragments is not provided, try to extract them from self.data.
+ if matched_fragments is None and hasattr(self, "data"):
+ df = self.data
+ # Check for column "ion_annotation" and either "ion_color" or "color_annotation"
+ color_col = "ion_color" if "ion_color" in df.columns else "color_annotation"
+ if "ion_annotation" in df.columns and color_col in df.columns:
+ matched_fragments = []
+ for _, row in df.iterrows():
+ annot = str(row.get("ion_annotation", "")).strip()
+ frag_color = row.get(color_col, "blue")
+ # Ensure frag_color is a string; if not, fallback.
+ if not isinstance(frag_color, str):
+ frag_color = "blue"
+ # Extract numeric index from annotation (e.g. "a3+").
+ if len(annot) > 1:
+ ion_type = annot[0].lower()
+ try:
+ ion_index = int(annot[1:].rstrip("+"))
+ except ValueError:
+ continue
+ frag_x = start_x + (ion_index - 1) * spacing
+ if ion_type in "abc":
+ y_offset = frag_len
+ elif ion_type in "xyz":
+ y_offset = -frag_len
+ else:
+ y_offset = 0
+ matched_fragments.append((annot, frag_color, frag_x, y_offset))
+ # Draw the fragments if any.
+ if matched_fragments:
+ for frag in matched_fragments:
+ if len(frag) == 2:
+ annot, frag_color = frag
+ frag_x = x
+ y_offset = frag_len
+ elif len(frag) >= 4:
+ annot, frag_color, frag_x, y_offset = frag
+ else:
+ continue
+
+ if not isinstance(frag_color, str):
+ frag_color = "blue"
+
+ ax.plot(
+ [frag_x, frag_x],
+ [y, y + y_offset],
+ clip_on=False,
+ color=frag_color,
+ transform=ax.transAxes,
+ )
+ ax.text(
+ frag_x,
+ y + (y_offset * 1.1),
+ annot,
+ color=frag_color,
+ fontsize=fontsize_frag,
+ ha="center",
+ va="bottom" if y_offset >= 0 else "top",
+ transform=ax.transAxes,
+ )
class MATPLOTLIBPeakMapPlot(MATPLOTLIB_MSPlot, PeakMapPlot):
diff --git a/pyopenms_viz/_plotly/core.py b/pyopenms_viz/_plotly/core.py
index b106a044..0c3618b0 100644
--- a/pyopenms_viz/_plotly/core.py
+++ b/pyopenms_viz/_plotly/core.py
@@ -619,6 +619,12 @@ def _prepare_data(self, df, label_suffix=" (ref)"):
self.reference_spectrum[self.by] + label_suffix
)
return df
+
+ def plot_peptide_sequence(self, peptide_sequence: str, matched_fragments=None):
+ """
+ Raises a NotImplementedError because peptide sequence plotting is not supported for Plotly.
+ """
+ raise NotImplementedError("Peptide sequence plotting is currently unsupported in the Plotly backend.")
class PLOTLYPeakMapPlot(PLOTLY_MSPlot, PeakMapPlot):
diff --git a/test/__snapshots__/test_peakmap_marginals/test_peakmap_marginals[ms_bokeh].html b/test/__snapshots__/test_peakmap_marginals/test_peakmap_marginals[ms_bokeh].html
index 112f1fa6..faeacc5a 100644
--- a/test/__snapshots__/test_peakmap_marginals/test_peakmap_marginals[ms_bokeh].html
+++ b/test/__snapshots__/test_peakmap_marginals/test_peakmap_marginals[ms_bokeh].html
@@ -18,10 +18,10 @@
-
+
-
-
+
-