@brainpilot/skills 0.0.6 → 0.0.7

package/skills/14_Writing/paper-writing/scripts/figure_templates.py

@@ -0,0 +1,315 @@
+"""
+Reusable Nature-journal figure templates.
+
+Each function creates a complete figure from data and saves it.
+Derived from nature-skills/nature-figure (MIT License, Copyright 2026 Yuan Yizhe).
+Source: https://github.com/Yuan1z0825/nature-skills
+"""
+
+import numpy as np
+import matplotlib
+matplotlib.use('Agg')
+import matplotlib.pyplot as plt
+import matplotlib as mpl
+from matplotlib import gridspec
+
+from nature_figure_style import (
+    apply_publication_style, DEFAULT_COLORS, DEFAULT_COLORS_NMI_PASTEL,
+    add_panel_label, is_dark, finalize_figure,
+)
+
+
+def make_grouped_bar(ax, categories, series, labels,
+                     ylabel='Value', colors=None,
+                     annotate=False, bar_width=0.8,
+                     error_kw=None):
+    """
+    Grouped bar chart.
+
+    Parameters
+    ----------
+    ax         : matplotlib Axes
+    categories : list[str]  — x-axis category names (length K)
+    series     : list[array] — one array per group (each length K)
+    labels     : list[str]  — legend label per group
+    colors     : list[str] | None
+    annotate   : bool  — print value above each bar
+    bar_width  : float — total width for all bars in one category
+    error_kw   : dict  — passed to ax.bar
+
+    Returns
+    -------
+    list[BarContainer]
+    """
+    if colors is None:
+        colors = DEFAULT_COLORS
+    if error_kw is None:
+        error_kw = {'elinewidth': 2, 'capthick': 2, 'capsize': 10}
+    n_groups = len(series)
+    n_cats = len(categories)
+    w = bar_width / n_groups
+    x = np.arange(n_cats)
+    containers = []
+    for i, (vals, label, color) in enumerate(zip(series, labels, colors)):
+        offset = (i - (n_groups - 1) / 2) * w
+        bars = ax.bar(x + offset, vals, width=w, label=label,
+                      color=color, edgecolor='black', linewidth=1.5,
+                      error_kw=error_kw)
+        containers.append(bars)
+        if annotate:
+            for bar, val in zip(bars, vals):
+                ax.text(bar.get_x() + bar.get_width() / 2,
+                        bar.get_height() + 0.01,
+                        f'{val:.2f}', ha='center', va='bottom', fontsize=10)
+    ax.set_xticks(x)
+    ax.set_xticklabels(categories)
+    ax.set_ylabel(ylabel)
+    ax.legend()
+    return containers
+
+
+def make_trend(ax, x, y_series, labels,
+               colors=None, ylabel=None, xlabel=None,
+               show_shadow=False, shadow_alpha=0.15,
+               lw=2.5, marker='o', markersize=8):
+    """
+    Multi-line trend plot.
+
+    Parameters
+    ----------
+    x        : array-like   — shared x values
+    y_series : list[array]  — one 1D array per line (or 2D for mean±std)
+    labels   : list[str]
+    show_shadow : bool  — fill_between ± std if y_series contains 2D arrays
+    """
+    if colors is None:
+        colors = DEFAULT_COLORS
+    for y, label, color in zip(y_series, labels, colors):
+        y = np.asarray(y)
+        if y.ndim == 2:
+            mean, std = y.mean(0), y.std(0)
+        else:
+            mean, std = y, None
+        ax.plot(x, mean, color=color, lw=lw, marker=marker,
+                markersize=markersize, label=label)
+        if show_shadow and std is not None:
+            ax.fill_between(x, mean - std, mean + std,
+                            color=color, alpha=shadow_alpha)
+    if ylabel:
+        ax.set_ylabel(ylabel)
+    if xlabel:
+        ax.set_xlabel(xlabel)
+    ax.legend()
+
+
+def make_forest_plot(ax, labels, estimates, ci_low, ci_high,
+                     colors=None, ref=0.0, xlabel=None, xlim=None,
+                     marker='o', markersize=5, lw=1.5):
+    """Minimal forest plot for Nature-style clinical/statistical panels."""
+    y = np.arange(len(labels))[::-1]
+    if colors is None:
+        colors = ['#B64342'] * len(labels)
+    for yi, est, lo, hi, color in zip(y, estimates, ci_low, ci_high, colors):
+        ax.plot([lo, hi], [yi, yi], color=color, lw=lw)
+        ax.plot(est, yi, marker=marker, ms=markersize, color=color)
+    ax.axvline(ref, color='#767676', linestyle='--', linewidth=1.2, alpha=0.8)
+    ax.set_yticks(y)
+    ax.set_yticklabels(labels)
+    if xlabel:
+        ax.set_xlabel(xlabel)
+    if xlim is not None:
+        ax.set_xlim(xlim)
+    ax.spines['right'].set_visible(False)
+    ax.spines['top'].set_visible(False)
+
+
+def make_heatmap(ax, matrix, x_labels=None, y_labels=None,
+                 cmap='magma', cbar_label=None, annotate=False,
+                 fmt='{:.2f}', fontsize=12):
+    """2D heatmap with optional colorbar and cell annotations."""
+    im = ax.imshow(matrix, cmap=cmap, aspect='auto')
+    if cbar_label:
+        cbar = ax.figure.colorbar(im, ax=ax)
+        cbar.set_label(cbar_label)
+    if x_labels:
+        ax.set_xticks(range(len(x_labels)))
+        ax.set_xticklabels(x_labels, rotation=30, ha='right')
+    if y_labels:
+        ax.set_yticks(range(len(y_labels)))
+        ax.set_yticklabels(y_labels)
+    if annotate:
+        norm = mpl.colors.Normalize(vmin=matrix.min(), vmax=matrix.max())
+        cm_obj = plt.get_cmap(cmap)
+        for (i, j), val in np.ndenumerate(matrix):
+            r, g, b, _ = cm_obj(norm(val))
+            lum = 0.299 * r + 0.587 * g + 0.114 * b
+            color = 'white' if lum < 0.5 else 'black'
+            ax.text(j, i, fmt.format(val), ha='center', va='center',
+                    fontsize=fontsize, color=color)
+    ax.set_frame_on(False)
+
+
+# ─────────────────────────────────────────────────────────────────────────────
+# Complete Figure Templates
+# ─────────────────────────────────────────────────────────────────────────────
+
+def template_grouped_bar_with_legend_panel(methods, metrics, mean_dict, std_dict,
+                                           colors=None, out_path='./figures/comparison'):
+    """
+    Multi-metric grouped bar chart with a dedicated legend panel.
+
+    Parameters
+    ----------
+    methods   : list[str]       — method names
+    metrics   : list[str]       — metric names
+    mean_dict : dict[str,array] — metric -> array of means per method
+    std_dict  : dict[str,array] — metric -> array of stds per method
+    colors    : list[str]       — one color per method
+    out_path  : str             — save path (no extension)
+    """
+    apply_publication_style(font_size=24, axes_linewidth=3)
+    if colors is None:
+        colors = DEFAULT_COLORS[:len(methods)]
+
+    fig = plt.figure(figsize=(28, 6))
+    gs = gridspec.GridSpec(1, len(metrics) + 1)
+
+    handles, labels = None, None
+    for col, metric in enumerate(metrics):
+        ax = fig.add_subplot(gs[col])
+        bars = ax.bar(
+            range(len(methods)), mean_dict[metric],
+            yerr=std_dict[metric], capsize=5,
+            color=colors, label=methods,
+            error_kw={'elinewidth': 2, 'capthick': 2},
+        )
+        if col == 0:
+            handles, labels = ax.get_legend_handles_labels()
+        ax.set_xticks([])
+        y_vals = mean_dict[metric]
+        margin = (y_vals.max() - y_vals.min()) * 0.15
+        ax.set_ylim([y_vals.min() - margin, y_vals.max() + margin])
+        ax.set_ylabel(metric, fontsize=32)
+
+    ax_leg = fig.add_subplot(gs[-1])
+    ax_leg.legend(handles, labels, fontsize=28, loc='center', frameon=False)
+    ax_leg.set_axis_off()
+
+    return finalize_figure(fig, out_path, formats=['png', 'pdf'])
+
+
+def template_ablation_bar(configs, values, stds=None,
+                          out_path='./figures/ablation'):
+    """
+    Horizontal ablation bar chart with alpha-graduated colors.
+
+    Parameters
+    ----------
+    configs : list[str] — ablation configuration names
+    values  : array      — performance values
+    stds    : array|None  — standard deviations
+    """
+    apply_publication_style(font_size=24, axes_linewidth=3)
+
+    n = len(configs)
+    blue_rgb = (0.215686, 0.458824, 0.729412)
+    alphas = np.linspace(0.2, 1.0, n)
+    colors = [(blue_rgb[0], blue_rgb[1], blue_rgb[2], a) for a in alphas]
+
+    fig, ax = plt.subplots(figsize=(12, 6))
+    ax.barh(range(n), values, xerr=stds, color=colors, ecolor='k', capsize=5)
+    ax.set_yticks(range(n))
+    ax.set_yticklabels(configs)
+    ax.set_xlim([values.min() - 0.05, values.max() + 0.03])
+    ax.set_xlabel('Score', fontsize=32)
+
+    return finalize_figure(fig, out_path, formats=['png'])
+
+
+def template_multi_panel_trend(methods, x, y_dict, panel_names,
+                               colors=None, out_path='./figures/trends'):
+    """
+    Multi-panel trend plot with shared legend panel.
+
+    Parameters
+    ----------
+    methods     : list[str]
+    x           : array — shared x values
+    y_dict      : dict[str, list[array]] — panel_name -> list of y arrays per method
+    panel_names : list[str]
+    colors      : list[str]
+    """
+    apply_publication_style(font_size=15, axes_linewidth=2)
+    if colors is None:
+        colors = DEFAULT_COLORS[:len(methods)]
+
+    fig, axes = plt.subplots(1, len(panel_names) + 1, figsize=(18, 5))
+    handles, labels = None, None
+
+    for idx, (ax, name) in enumerate(zip(axes[:len(panel_names)], panel_names)):
+        for method, color in zip(methods, colors):
+            y = y_dict[name][method]
+            ax.plot(x, y, color=color, lw=2.5, marker='o', markersize=6, label=method)
+        ax.set_title(name, fontsize=18)
+        ax.set_xlabel('Epoch', fontsize=16)
+        ax.set_ylabel('Loss', fontsize=16)
+        if idx == 0:
+            handles, labels = ax.get_legend_handles_labels()
+
+    axes[-1].legend(handles, labels, fontsize=14, loc='center', frameon=False)
+    axes[-1].set_axis_off()
+
+    return finalize_figure(fig, out_path, formats=['png', 'pdf'])
+
+
+def template_dual_colormap_heatmap(matrix, methods, metrics,
+                                    out_path='./figures/heatmap'):
+    """
+    Heatmap with dual colormaps (positive=Reds, negative=Blues_r).
+
+    Parameters
+    ----------
+    matrix   : 2D array — rows=methods, cols=metrics
+    methods  : list[str]
+    metrics  : list[str] — even indices positive, odd indices negative
+    """
+    apply_publication_style(font_size=16, axes_linewidth=2)
+
+    fig, ax = plt.subplots(figsize=(10, 6))
+    n_rows, n_cols = matrix.shape
+    vmax = matrix.max(0)
+
+    for j in range(n_cols):
+        is_positive = (j % 2 == 0)
+        cmap = plt.cm.Reds if is_positive else plt.cm.Blues_r
+        cmap = cmap.copy()
+        norm = mpl.colors.Normalize(
+            vmin=0 if is_positive else vmax[j],
+            vmax=vmax[j] if is_positive else 0,
+        )
+        ax.imshow(matrix[:, j:j + 1], cmap=cmap, norm=norm,
+                  aspect='auto', extent=[j - 0.5, j + 0.5, 0, n_rows], origin='lower')
+
+    for (i, j), val in np.ndenumerate(matrix):
+        is_positive = (j % 2 == 0)
+        cmap = plt.cm.Reds if is_positive else plt.cm.Blues_r
+        norm = mpl.colors.Normalize(
+            vmin=0 if is_positive else vmax[j],
+            vmax=vmax[j] if is_positive else 0,
+        )
+        r, g, b, _ = cmap(norm(val))
+        lum = 0.299 * r + 0.587 * g + 0.114 * b
+        color = 'white' if lum < 0.5 else 'black'
+        ax.text(j, i + 0.5, f'{val:.2f}', ha='center', va='center',
+                fontsize=13, color=color)
+
+    ax.set_xlim(-0.5, n_cols - 0.5)
+    ax.set_xticks(np.arange(n_cols))
+    ax.set_xticklabels(metrics, rotation=30, ha='right', fontsize=14)
+    ax.tick_params(axis='x', bottom=False, top=False, length=0)
+    ax.set_yticks(np.arange(n_rows) + 0.5)
+    ax.set_yticklabels(methods, fontsize=14)
+    ax.set_frame_on(False)
+    ax.invert_yaxis()
+
+    return finalize_figure(fig, out_path, formats=['png'])

package/skills/14_Writing/paper-writing/scripts/nature_figure_style.py

@@ -0,0 +1,214 @@
+"""
+Nature-journal publication style constants and helper functions.
+
+Derived from nature-skills/nature-figure (MIT License, Copyright 2026 Yuan Yizhe).
+Source: https://github.com/Yuan1z0825/nature-skills
+"""
+
+import matplotlib
+matplotlib.use('Agg')
+import matplotlib.pyplot as plt
+import numpy as np
+import os
+from pathlib import Path
+
+
+# ─────────────────────────────────────────────────────────────────────────────
+# Color Palettes
+# ─────────────────────────────────────────────────────────────────────────────
+
+PALETTE = {
+    "blue_main":      "#0F4D92",
+    "blue_secondary": "#3775BA",
+    "green_1": "#DDF3DE",
+    "green_2": "#AADCA9",
+    "green_3": "#8BCF8B",
+    "red_1":   "#F6CFCB",
+    "red_2":   "#E9A6A1",
+    "red_strong": "#B64342",
+    "neutral_light": "#CFCECE",
+    "neutral_mid":   "#767676",
+    "neutral_dark":  "#4D4D4D",
+    "neutral_black": "#272727",
+    "gold":   "#FFD700",
+    "teal":   "#42949E",
+    "violet": "#9A4D8E",
+    "magenta":"#EA84DD",
+}
+
+DEFAULT_COLORS = [
+    PALETTE["blue_main"],
+    PALETTE["green_3"],
+    PALETTE["red_strong"],
+    PALETTE["teal"],
+    PALETTE["violet"],
+    PALETTE["neutral_light"],
+]
+
+PALETTE_NMI_PASTEL = {
+    "baseline_dark": "#484878",
+    "baseline_mid":  "#7884B4",
+    "baseline_soft": "#B4C0E4",
+    "ours_tiny":  "#E4E4F0",
+    "ours_base":  "#E4CCD8",
+    "ours_large": "#F0C0CC",
+    "bg_lilac": "#E0E0F0",
+    "bg_aqua":  "#E0F0F0",
+    "bg_peach": "#F0E0D0",
+    "neutral_light": "#D8D8D8",
+    "neutral_mid":   "#A8A8A8",
+    "neutral_dark":  "#606060",
+    "delta_up":   "#2E9E44",
+    "delta_down": "#E53935",
+}
+
+DEFAULT_COLORS_NMI_PASTEL = [
+    PALETTE_NMI_PASTEL["baseline_dark"],
+    PALETTE_NMI_PASTEL["baseline_mid"],
+    PALETTE_NMI_PASTEL["baseline_soft"],
+    PALETTE_NMI_PASTEL["ours_tiny"],
+    PALETTE_NMI_PASTEL["ours_base"],
+    PALETTE_NMI_PASTEL["ours_large"],
+]
+
+PALETTE_NATURE_IMAGING = {
+    "bg": "#000000",
+    "context": "#B8B8B8",
+    "cyan": "#22D7E6",
+    "magenta": "#FF2AD4",
+    "white": "#FFFFFF",
+}
+
+PALETTE_NATURE_MATERIAL = {
+    "aqua": "#77D7D1",
+    "teal": "#33B5A5",
+    "lilac": "#B9A7E8",
+    "violet": "#7C6CCF",
+    "callout_red": "#E53935",
+    "neutral": "#D9D9D9",
+}
+
+PALETTE_NATURE_CLINICAL = {
+    "baseline": "#272727",
+    "week6": "#E28E2C",
+    "week13": "#D24B40",
+    "week26": "#5B8FD6",
+    "year1": "#7BAA5B",
+    "year2": "#C45AD6",
+    "group_band": "#F2E6D9",
+}
+
+PALETTE_NATURE_GENOMICS = {
+    "neutral_light": "#D8D8D8",
+    "neutral_mid": "#8F8F8F",
+    "wave1": "#D9544D",
+    "wave2": "#5B7FCA",
+    "wave3": "#B89BD9",
+    "outline": "#4D4D4D",
+}
+
+
+# ─────────────────────────────────────────────────────────────────────────────
+# Style Setup
+# ─────────────────────────────────────────────────────────────────────────────
+
+def apply_publication_style(font_size=16, axes_linewidth=2.5, use_tex=False):
+    """Apply Nature-style rcParams. Call once before creating any figures."""
+    plt.rcParams['font.family'] = 'sans-serif'
+    plt.rcParams['font.sans-serif'] = ['Arial', 'DejaVu Sans', 'Liberation Sans']
+    plt.rcParams['svg.fonttype'] = 'none'
+    plt.rcParams['font.size'] = font_size
+    plt.rcParams['axes.spines.right'] = False
+    plt.rcParams['axes.spines.top'] = False
+    plt.rcParams['axes.linewidth'] = axes_linewidth
+    plt.rcParams['legend.frameon'] = False
+    if use_tex:
+        plt.rcParams['text.usetex'] = True
+
+
+# Presets:
+#   Large bar panels:      apply_publication_style(font_size=24, axes_linewidth=3)
+#   Compact figures:       apply_publication_style(font_size=15, axes_linewidth=2)
+#   Dense multi-panels:    apply_publication_style(font_size=8, axes_linewidth=1)
+#   LaTeX labels:          apply_publication_style(use_tex=True)
+
+
+# ─────────────────────────────────────────────────────────────────────────────
+# Helper Functions
+# ─────────────────────────────────────────────────────────────────────────────
+
+def is_dark(hex_color, threshold=128):
+    """Return True if hex color is dark (use white text on it)."""
+    c = hex_color.lstrip('#')
+    r, g, b = int(c[0:2], 16), int(c[2:4], 16), int(c[4:6], 16)
+    return (0.299 * r + 0.587 * g + 0.114 * b) < threshold
+
+
+def add_panel_label(ax, label, x=-0.06, y=1.02, fontsize=14,
+                    color='black', fontweight='bold'):
+    """Place a Nature-style panel label near the top-left edge."""
+    ax.text(
+        x, y, label,
+        transform=ax.transAxes,
+        fontsize=fontsize,
+        fontweight=fontweight,
+        color=color,
+        ha='left',
+        va='bottom',
+    )
+
+
+def style_dark_image_ax(ax, facecolor='black'):
+    """Prepare an axes for microscopy / rendering plates."""
+    ax.set_facecolor(facecolor)
+    ax.set_xticks([])
+    ax.set_yticks([])
+    for spine in ax.spines.values():
+        spine.set_visible(False)
+    return ax
+
+
+def annotate_bars(ax, bars, colors, fmt='{:.2f}', fontsize=32, offset=-0.10):
+    """Add luminance-aware text labels on bars."""
+    for bar, color in zip(bars, colors):
+        c = color.lstrip('#')
+        r, g, b = int(c[0:2], 16) / 255, int(c[2:4], 16) / 255, int(c[4:6], 16) / 255
+        lum = 0.299 * r + 0.587 * g + 0.114 * b
+        textcolor = 'white' if lum < 0.5 else 'black'
+        value = bar.get_height()
+        ax.text(bar.get_x() + bar.get_width() / 2,
+                value + offset,
+                fmt.format(value),
+                ha='center', va='bottom',
+                fontsize=fontsize, color=textcolor)
+
+
+def finalize_figure(fig, out_path, formats=None, dpi=300,
+                    pad=2, bbox_inches=None, close=True):
+    """
+    Apply tight_layout and save figure.
+
+    Parameters
+    ----------
+    out_path : str   — path without extension, or with extension
+    formats  : list  — e.g. ['png', 'pdf']. If None, uses extension of out_path.
+    dpi      : int   — 300 standard, 600 for dense bar panels
+    pad      : float — tight_layout pad (2 default, 1 for compact multi-panel)
+    """
+    fig.tight_layout(pad=pad)
+    base = Path(out_path)
+    os.makedirs(base.parent, exist_ok=True)
+    if formats is None:
+        formats = [base.suffix.lstrip('.') or 'png']
+        base = base.with_suffix('')
+    saved = []
+    for fmt in formats:
+        p = str(base) + f'.{fmt}'
+        kw = {}
+        if bbox_inches is not None:
+            kw['bbox_inches'] = bbox_inches
+        fig.savefig(p, dpi=dpi, **kw)
+        saved.append(p)
+    if close:
+        plt.close(fig)
+    return saved