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Enhance x-tick label customization: add font size, color, and rotatio… #2

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Merged
sanjaysgk merged 1 commit into from
Jun 19, 2025
Merged

Enhance x-tick label customization: add font size, color, and rotatio… #2

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2 changes: 1 addition & 1 deletion ProtPeptigram/runner.py
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Original file line number Diff line number Diff line change
Expand Up @@ -184,7 +184,7 @@ def run_pipeline(
group_by='Sample',
color_by='protein',
figsize=(14, 12),
title=f"Peptide Visualization - {prot}",
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@sourcery-ai sourcery-ai bot Jun 19, 2025

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nitpick (typo): Title spelling is inconsistent with US/UK English conventions.

Consider updating the spelling to match the convention used elsewhere in the project.

Suggested change
title=f"Peptide Visualization - {prot}",
title=f"Peptide-Protein alignment visualization - {prot}",

title=f"Peptide-Protein alignment visualisation - {prot}",
color_by_protein_and_intensity=False,
intensity_cmaps=["Blues", "Reds", "Greens", "Purples"],
protein_cmap="Set1",
Expand Down
28 changes: 23 additions & 5 deletions ProtPeptigram/viz.py
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Original file line number Diff line number Diff line change
Expand Up @@ -50,6 +50,9 @@ def plot_peptigram(
title: Optional[str] = None,
x_lab_forntsize: int = 12,
y_lab_forntsize: int = 12,
xticks_font: int = 12,
xticks_color: str = "#333333",
xticks_rotation: int = 0,
Comment on lines +53 to +55
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suggestion: Parameter naming is inconsistent between function signature and docstring.

The docstring uses 'x_ticks_rotation' while the parameter is 'xticks_rotation'. Please use the same name in both for clarity.

Suggested implementation:

        x_ticks_rotation: int = 0,
        """
        Create a PeptiGram visualization with protein-based coloring.

            Font size for x-axis labels Amino acid positions(default: 12)
            x_ticks_rotation: int
                Rotation angle for x-axis tick labels (default: 0)
        # ... (usage in function body)
        ax.set_xticklabels(labels, fontsize=xticks_font, color=xticks_color, rotation=x_ticks_rotation)

annotate: bool = True,
min_intensity: Optional[float] = None,
highlight_regions: Optional[List[Tuple[int, int]]] = None,
Expand All @@ -65,7 +68,7 @@ def plot_peptigram(
highlight_alpha: float = 0.25,
highlight_color: str = "#FF8888",
dpi: int = 300
):
) -> Tuple[plt.Figure, List[plt.Axes]]:
"""
Create a PeptiGram visualization with protein-based coloring.

Expand All @@ -87,6 +90,12 @@ def plot_peptigram(
Font size for x-axis labels Amino acid positions(default: 12)
y_lab_forntsize : int, optional
Font size for y-axis labels Sample names and Density plot(default: 12)
xticks_font : int, optional
Font size for x-axis tick labels (default: 12)
xticks_color : str, optional
Color for x-axis tick labels (default: "#333333")
x_ticks_rotation : int, optional
Rotation angle for x-axis tick labels (default: 0)
annotate : bool, optional
Whether to annotate proteins (default: True)
min_intensity : float, optional
Expand Down Expand Up @@ -315,7 +324,7 @@ def plot_peptigram(
# Get color for this protein
protein_color = protein_to_color[protein_id]

# Plot density with publication-quality styling
# Plot density with high quality styling
axs[0].bar(positions, density, color=protein_color, alpha=0.75, width=1,
label=protein_id, edgecolor=None, linewidth=0)

Expand Down Expand Up @@ -537,7 +546,7 @@ def plot_peptigram(
space_needed = spaces[height, space_start:space_end+1]
if np.sum(space_needed) == 0: # Space is available
spaces[height, space_start:space_end+1] = 1
# Publication-quality peptide visualization
#peptide visualization
ax.plot(
[start, end],
[-height-0.4, -height-0.4],
Expand Down Expand Up @@ -586,7 +595,6 @@ def plot_peptigram(
linestyle='-', alpha=0.3, linewidth=0.8)
ax.axvline(end, color=highlight_color,
linestyle='-', alpha=0.3, linewidth=0.8)

# Set title
if title is None:
if len(protein_ids) == 1:
Expand All @@ -604,7 +612,7 @@ def plot_peptigram(
protein_str = protein_str[:47] + "..."
plt.figtext(0.5, 0.94, protein_str, ha='center', color=text_color,
fontsize=9, fontstyle='italic')

# Add subtitle for coloring method
coloring_method = ""
if color_by_protein_and_intensity:
Expand Down Expand Up @@ -635,6 +643,16 @@ def plot_peptigram(
plt.figtext(0.5, y_pos, f"Auto-highlighted regions: {regions_str}",
ha='center', fontsize=9, fontstyle='italic', color=highlight_color)

# Handle x-tick labels for all axes except the last one
for i in range(len(axs)):
# if i == 0: # Density plot - keep labels
# continue
if i == len(axs) - 1: # Last plot - keep labels
axs[i].tick_params(axis='x', labelsize=xticks_font, rotation=xticks_rotation, labelcolor=xticks_color)
else: # Middle plots - hide labels
axs[i].tick_params(axis='x', labelbottom=False)


# Set x-label on the bottom axis only
axs[-1].set_xlabel('Amino Acid Position',
fontweight='normal', color=text_color, fontsize=x_lab_forntsize)
Expand Down