feat(plotly): implement sequence-logo-basic

plots/sequence-logo-basic/implementations/plotly.py

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+""" pyplots.ai
+sequence-logo-basic: Sequence Logo for Motif Visualization
+Library: plotly 6.6.0 | Python 3.14.3
+Quality: 86/100 | Created: 2026-03-06
+"""
+
+import numpy as np
+import plotly.graph_objects as go
+
+
+# Data - transcription factor binding site motif (10-position DNA)
+# Position weight matrix: each row is [A, C, G, T] frequencies
+pwm = np.array(
+    [
+        [0.05, 0.80, 0.05, 0.10],  # pos 1: C dominant
+        [0.10, 0.15, 0.10, 0.65],  # pos 2: T dominant
+        [0.02, 0.96, 0.01, 0.01],  # pos 3: C highly conserved (~1.8 bits)
+        [0.25, 0.25, 0.25, 0.25],  # pos 4: uniform (0 bits)
+        [0.70, 0.05, 0.15, 0.10],  # pos 5: A dominant
+        [0.10, 0.10, 0.70, 0.10],  # pos 6: G dominant
+        [0.001, 0.001, 0.001, 0.997],  # pos 7: T near-perfect conservation (~1.97 bits)
+        [0.60, 0.15, 0.15, 0.10],  # pos 8: A dominant
+        [0.10, 0.10, 0.65, 0.15],  # pos 9: G dominant
+        [0.15, 0.55, 0.10, 0.20],  # pos 10: C dominant
+    ]
+)
+
+letters = ["A", "C", "G", "T"]
+# Standard DNA sequence logo colors: A=green, C=blue, G=orange, T=red
+# Using colorblind-safe Wong palette variants
+colors = {"A": "#009E73", "C": "#0072B2", "G": "#E69F00", "T": "#D55E00"}
+n_positions = len(pwm)
+
+# Information content: IC = 2 + sum(f * log2(f)) for DNA (max 2 bits)
+info_content = np.zeros(n_positions)
+for i in range(n_positions):
+    entropy = sum(f * np.log2(f) for f in pwm[i] if f > 0)
+    info_content[i] = max(0, 2.0 + entropy)
+
+# Letter heights = frequency * information content at each position
+letter_heights = pwm * info_content[:, np.newaxis]
+
+# SVG path data for letters (simplified block-style glyphs within 0-1 x 0-1 box)
+letter_paths = {
+    "A": "M 0.5 0 L 0.05 1 L 0.25 1 L 0.35 0.7 L 0.65 0.7 L 0.75 1 L 0.95 1 L 0.5 0 Z M 0.4 0.52 L 0.6 0.52 L 0.55 0.38 L 0.45 0.38 Z",
+    "C": "M 0.85 0.2 C 0.65 -0.05 0.2 0 0.1 0.3 C 0 0.6 0.15 0.95 0.5 1 C 0.7 1.02 0.85 0.9 0.88 0.8 L 0.68 0.7 C 0.6 0.82 0.5 0.82 0.4 0.78 C 0.28 0.7 0.25 0.5 0.3 0.35 C 0.35 0.2 0.5 0.15 0.6 0.18 C 0.68 0.2 0.72 0.28 0.75 0.32 Z",
+    "G": "M 0.85 0.2 C 0.65 -0.05 0.2 0 0.1 0.3 C 0 0.6 0.15 0.95 0.5 1 C 0.7 1.02 0.85 0.9 0.88 0.8 L 0.68 0.7 C 0.6 0.82 0.5 0.82 0.4 0.78 C 0.28 0.7 0.25 0.5 0.3 0.35 C 0.35 0.2 0.5 0.15 0.6 0.18 C 0.68 0.2 0.72 0.28 0.75 0.32 L 0.85 0.2 Z M 0.55 0.45 L 0.85 0.45 L 0.85 0.55 L 0.55 0.55 Z",
+    "T": "M 0.05 0 L 0.05 0.18 L 0.38 0.18 L 0.38 1 L 0.62 1 L 0.62 0.18 L 0.95 0.18 L 0.95 0 Z",
+}
+
+# Plot - using Plotly shapes for stretched letter glyphs
+fig = go.Figure()
+bar_width = 0.38  # half-width for shapes
+
+# Build letter shapes at each position
+for pos in range(n_positions):
+    heights = letter_heights[pos]
+    sorted_indices = np.argsort(heights)
+    y_bottom = 0
+
+    for idx in sorted_indices:
+        h = heights[idx]
+        if h < 0.005:
+            continue
+        letter = letters[idx]
+
+        # Add invisible bar for hover interaction
+        fig.add_trace(
+            go.Bar(
+                x=[pos + 1],
+                y=[h],
+                base=y_bottom,
+                width=bar_width * 2,
+                marker={"color": "rgba(0,0,0,0)", "line": {"width": 0}},
+                showlegend=False,
+                hovertemplate=(
+                    f"<b>Position {pos + 1}</b><br>"
+                    f"Nucleotide: {letter}<br>"
+                    f"Frequency: {pwm[pos][idx]:.0%}<br>"
+                    f"Height: {h:.3f} bits"
+                    f"<extra></extra>"
+                ),
+            )
+        )
+
+        # Transform SVG path from 0-1 space to data coordinates (inline)
+        tokens = letter_paths[letter].split()
+        path_parts = []
+        ti = 0
+        while ti < len(tokens):
+            cmd = tokens[ti]
+            if cmd in ("M", "L", "Z"):
+                path_parts.append(cmd)
+                if cmd != "Z":
+                    px = float(tokens[ti + 1])
+                    py = float(tokens[ti + 2])
+                    path_parts.append(str((pos + 1) - bar_width + px * 2 * bar_width))
+                    path_parts.append(str(y_bottom + py * h))
+                    ti += 3
+                else:
+                    ti += 1
+            elif cmd == "C":
+                path_parts.append(cmd)
+                for j in range(3):
+                    px = float(tokens[ti + 1 + j * 2])
+                    py = float(tokens[ti + 2 + j * 2])
+                    path_parts.append(str((pos + 1) - bar_width + px * 2 * bar_width))
+                    path_parts.append(str(y_bottom + py * h))
+                ti += 7
+            else:
+                ti += 1
+        path_data = " ".join(path_parts)
+
+        fig.add_shape(
+            type="path",
+            path=path_data,
+            fillcolor=colors[letter],
+            line={"width": 0.5, "color": colors[letter]},
+            layer="above",
+            xref="x",
+            yref="y",
+        )
+
+        y_bottom += h
+
+# Legend entries
+for letter in letters:
+    fig.add_trace(
+        go.Scatter(
+            x=[None],
+            y=[None],
+            mode="markers",
+            marker={"size": 18, "color": colors[letter], "symbol": "square"},
+            name=f"  {letter}  ",
+            showlegend=True,
+        )
+    )
+
+# Style
+fig.update_layout(
+    title={
+        "text": "sequence-logo-basic · plotly · pyplots.ai",
+        "font": {"size": 28, "family": "Arial, Helvetica, sans-serif", "color": "#1a1a2e"},
+        "x": 0.5,
+        "y": 0.96,
+    },
+    xaxis={
+        "title": {
+            "text": "Position",
+            "font": {"size": 22, "color": "#1a1a2e", "family": "Arial, sans-serif"},
+            "standoff": 12,
+        },
+        "tickfont": {"size": 18, "color": "#4a4a68", "family": "Arial, sans-serif"},
+        "tickvals": list(range(1, n_positions + 1)),
+        "showline": True,
+        "linewidth": 2,
+        "linecolor": "#1a1a2e",
+        "mirror": False,
+        "showgrid": False,
+        "zeroline": False,
+        "ticks": "outside",
+        "ticklen": 8,
+        "tickwidth": 1.5,
+        "tickcolor": "#4a4a68",
+    },
+    yaxis={
+        "title": {
+            "text": "Information content (bits)",
+            "font": {"size": 22, "color": "#1a1a2e", "family": "Arial, sans-serif"},
+            "standoff": 10,
+        },
+        "tickfont": {"size": 18, "color": "#4a4a68", "family": "Arial, sans-serif"},
+        "range": [0, 2.15],
+        "showline": True,
+        "linewidth": 2,
+        "linecolor": "#1a1a2e",
+        "mirror": False,
+        "gridwidth": 0.5,
+        "gridcolor": "rgba(100,100,140,0.08)",
+        "griddash": "dot",
+        "zeroline": True,
+        "zerolinewidth": 2,
+        "zerolinecolor": "#1a1a2e",
+        "ticks": "outside",
+        "ticklen": 8,
+        "tickwidth": 1.5,
+        "tickcolor": "#4a4a68",
+        "dtick": 0.5,
+    },
+    template="plotly_white",
+    barmode="overlay",
+    bargap=0,
+    plot_bgcolor="white",
+    paper_bgcolor="white",
+    legend={
+        "font": {"size": 20, "family": "Arial Black, Impact, sans-serif"},
+        "orientation": "h",
+        "yanchor": "bottom",
+        "y": 1.04,
+        "xanchor": "center",
+        "x": 0.5,
+        "bgcolor": "rgba(0,0,0,0)",
+        "tracegroupgap": 20,
+    },
+    margin={"l": 90, "r": 50, "t": 120, "b": 70},
+    hoverlabel={"bgcolor": "white", "bordercolor": "#4a4a68", "font": {"size": 15, "family": "Arial, sans-serif"}},
+)
+
+# Annotate highly conserved positions with larger, more prominent labels
+conserved_positions = [2, 6]  # positions 3 and 7 (0-indexed)
+for pos_idx in conserved_positions:
+    ic_val = info_content[pos_idx]
+    fig.add_annotation(
+        x=pos_idx + 1,
+        y=ic_val + 0.08,
+        text=f"▼ {ic_val:.2f} bits",
+        font={
+            "size": 16,
+            "color": "#1a1a2e",
+            "family": "Arial, sans-serif",
+            "weight": "bold" if ic_val > 1.9 else "normal",
+        },
+        showarrow=False,
+        yanchor="bottom",
+        xanchor="center",
+    )
+
+# Add subtle annotation for the zero-information position
+fig.add_annotation(
+    x=4,
+    y=-0.08,
+    text="no signal",
+    font={"size": 13, "color": "#999999", "family": "Arial, sans-serif"},
+    showarrow=False,
+    yanchor="top",
+    xanchor="center",
+)
+
+# Save
+fig.write_html("plot.html")
+fig.write_image("plot.png", width=1600, height=900, scale=3)