Generate Publication Figures

Skill: Generate Publication-Quality Figures

Purpose

Create matplotlib figures that meet journal submission standards: correct fonts, compact sizes, consistent styling, readable labels, and high DPI. Based on lessons learned from the CPA and TPflash papers (Fluid Phase Equilibria 2026).

SI Units (MANDATORY)

All figure axis labels MUST use SI units. See PAPER_WRITING_GUIDELINES.md "SI Units (MANDATORY)" for the full reference.

"bar" is acceptable for pressure axes in engineering contexts (1 bar = 100 kPa).

When to Use

• Creating figures for any scientific paper in the paperlab
• Regenerating figures after data or style revisions
• Setting up a new 02_generate_figures.py for a paper project

Core Setup (Copy-Paste Starter)

Every figure script should start with this rc configuration:

import matplotlib
matplotlib.use("Agg")
import matplotlib.pyplot as plt
import matplotlib.ticker as ticker
import numpy as np
import json
from pathlib import Path

# ── Publication-quality defaults ──────────────────────────────────
plt.rcParams.update({
    "font.family": "serif",
    "font.serif": ["Times New Roman", "DejaVu Serif"],
    "font.size": 9,
    "axes.titlesize": 10,
    "axes.labelsize": 9,
    "xtick.labelsize": 8,
    "ytick.labelsize": 8,
    "legend.fontsize": 8,
    "figure.dpi": 300,
    "savefig.dpi": 300,
    "savefig.bbox_inches": "tight",
    "axes.linewidth": 0.6,
    "xtick.direction": "in",
    "ytick.direction": "in",
    "xtick.major.size": 3,
    "ytick.major.size": 3,
    "xtick.minor.size": 1.5,
    "ytick.minor.size": 1.5,
    "grid.linewidth": 0.3,
    "grid.alpha": 0.4,
    "lines.linewidth": 1.0,
    "lines.markersize": 4,
})

# Consistent color palette
BLUE = "#2171b5"
ORANGE = "#e6550d"
GREEN = "#31a354"
GREY = "#636363"
PALETTE = [BLUE, ORANGE, GREEN, "#756bb1", "#e7298a", "#66a61e"]

# Output directory
FIGURES_DIR = Path(__file__).parent.parent / "figures"
FIGURES_DIR.mkdir(exist_ok=True)

Journal Column Widths

Size figures for the target journal's column width:

# Figure size templates
FIG_SINGLE = (3.5, 2.8)    # Single-column: width, height
FIG_SINGLE_TALL = (3.5, 3.5)
FIG_DOUBLE = (7.0, 3.5)    # Double-column
FIG_DOUBLE_TALL = (7.0, 5.0)

Common Figure Patterns

Pattern 1: Bar Chart (Comparison Across Categories)

fig, ax = plt.subplots(figsize=FIG_DOUBLE)
x = np.arange(len(categories))
w = 0.35
bars1 = ax.bar(x - w/2, values_a, w, color=BLUE, edgecolor="white", lw=0.3, label="Method A")
bars2 = ax.bar(x + w/2, values_b, w, color=ORANGE, edgecolor="white", lw=0.3, label="Method B")

ax.set_xticks(x)
ax.set_xticklabels(short_labels, rotation=0)  # NEVER rotate > 30°
ax.set_ylabel("Metric (unit)")
ax.legend(frameon=False, ncol=2)
ax.grid(axis="y", ls="--")
ax.set_axisbelow(True)
fig.savefig(FIGURES_DIR / "fig1_comparison.png")
plt.close()

Key rule: If category names are long, use short IDs (A1, A2, B1...) with a legend mapping below the figure or in the caption.

Pattern 2: Heatmap / Contour (2D Parameter Space)

fig, (ax1, ax2) = plt.subplots(1, 2, figsize=FIG_DOUBLE)

# Use pcolormesh for discrete data, contourf for smooth
im1 = ax1.pcolormesh(T_grid, P_grid, metric_grid_a, cmap="RdYlGn", shading="auto")
im2 = ax2.pcolormesh(T_grid, P_grid, metric_grid_b, cmap="RdYlGn", shading="auto")

for ax, title in zip([ax1, ax2], ["Method A", "Method B"]):
    ax.set_xlabel("$T$ (K)")
    ax.set_ylabel("$P$ (kPa)")
    ax.set_title(title, fontsize=9)

# Shared colorbar
fig.colorbar(im2, ax=[ax1, ax2], label="Iteration count", shrink=0.8, pad=0.02)
fig.savefig(FIGURES_DIR / "fig2_heatmap.png")
plt.close()

Key rule: NEVER use contour lines on noisy gridded data — they create ugly loops. Use pcolormesh instead. If overlaying contours, use very few levels (3–5) and ensure the data is smooth.

Pattern 3: Scatter with Per-Point Labels (Scaling)

When points cluster at the same x-value, labels will overlap. Use these techniques:

fig, ax = plt.subplots(figsize=FIG_SINGLE_TALL)

# 1. Define manual offsets per data point to prevent overlap
#    Format: {system_id: (dx, dy)} in data coordinates or points
offsets = {
    "A1": (5, -8), "A2": (5, 5), "B1": (-40, 5),
    "B2": (5, 3), "C1": (5, -8), "C2": (5, 5),
}

# 2. Jitter x-coordinates to separate clustered points
np.random.seed(42)
x_jitter = x_values + np.random.uniform(-0.15, 0.15, len(x_values))

ax.scatter(x_jitter, y_values, s=30, color=BLUE, zorder=5)

for i, (sid, xj, yv) in enumerate(zip(system_ids, x_jitter, y_values)):
    dx, dy = offsets.get(sid, (5, 3))
    ax.annotate(sid, (xj, yv), textcoords="offset points",
                xytext=(dx, dy), fontsize=7, color=GREY,
                arrowprops=dict(arrowstyle="-", color=GREY, lw=0.3) if abs(dx) > 10 else None)

ax.set_xlabel("Component count $N_c$")
ax.set_ylabel("Speedup factor")
ax.grid(True, ls="--")
fig.savefig(FIGURES_DIR / "fig4_scaling.png")
plt.close()

Key rules:

• ALWAYS check for label overlap visually — automated layouts (adjust_text) often fail
• For ≤15 points, define manual offsets dict during review
• Use short system IDs (A1, B3) not full names — put the legend in the caption

Pattern 4: Box Plot with Extreme Outliers

When data has a wide range (e.g., 1× to 30×), standard box plots compress the majority of the data. Solution: log scale.

fig, ax = plt.subplots(figsize=FIG_DOUBLE)

bp = ax.boxplot(data_by_group, labels=short_labels,
                patch_artist=True, showfliers=True, widths=0.5,
                medianprops=dict(color=ORANGE, lw=1.2),
                flierprops=dict(marker="o", ms=3, mfc="none", mec=GREY))

for patch in bp["boxes"]:
    patch.set_facecolor(BLUE)
    patch.set_alpha(0.35)

ax.set_yscale("log")  # Critical for wide-range data
ax.yaxis.set_major_formatter(ticker.FuncFormatter(lambda v, _: f"{v:.1f}" if v < 10 else f"{v:.0f}"))
ax.set_ylabel("Speedup factor")
ax.axhline(y=1.0, color="grey", ls="--", lw=0.6, label="Parity")
ax.grid(True, axis="y", ls="--")
ax.legend(frameon=False)
fig.savefig(FIGURES_DIR / "fig5_boxplot.png")
plt.close()

Key rule: Use log scale whenever max/min > 10. The linear scale will squash all boxes into a thin band at the bottom.

Pattern 5: Line Plot with Confidence Bands

fig, ax = plt.subplots(figsize=FIG_SINGLE)

ax.plot(x, y_mean, color=BLUE, lw=1.2, label="Mean")
ax.fill_between(x, y_low, y_high, color=BLUE, alpha=0.15, label="95% CI")
ax.plot(x_ref, y_ref, "o", color=ORANGE, ms=4, label="Reference data")

ax.set_xlabel("Temperature (K)")
ax.set_ylabel("Density (kg/m$^3$)")
ax.legend(frameon=False)
ax.grid(True, ls="--")
fig.savefig(FIGURES_DIR / "fig3_profile.png")
plt.close()

Pattern 6: Parity Plot (Calculated vs Reference)

fig, ax = plt.subplots(figsize=FIG_SINGLE)

ax.scatter(ref_values, calc_values, s=15, c=BLUE, alpha=0.6, edgecolors="none")

# Parity line
lims = [min(min(ref_values), min(calc_values)), max(max(ref_values), max(calc_values))]
ax.plot(lims, lims, "k--", lw=0.6, label="Parity")
# ±10% bands
ax.plot(lims, [l * 1.1 for l in lims], color=GREY, ls=":", lw=0.4)
ax.plot(lims, [l * 0.9 for l in lims], color=GREY, ls=":", lw=0.4)

ax.set_xlabel("Reference value")
ax.set_ylabel("Calculated value")
ax.set_aspect("equal")
ax.legend(frameon=False)
ax.grid(True, ls="--")
fig.savefig(FIGURES_DIR / "fig_parity.png")
plt.close()

Short System ID Convention

For papers with multiple test systems, use short IDs in figures and map them in a table in the paper:

Place the full table in the paper (usually Section 4: Benchmark Design) and reference it from figure captions: "System IDs are defined in Table 1."

Dual Output (PNG + PDF)

Always save both raster (PNG) and vector (PDF) versions. Journals prefer vector for line art but PNG is needed for Word embedding:

fig.savefig(FIGURES_DIR / "fig1_comparison.png")
fig.savefig(FIGURES_DIR / "fig1_comparison.pdf")

Figure Quality Checklist

Before finalizing any figure:

• Readable at print size: Text ≥ 7pt when printed at journal column width
• No label overlap: Check scatter plots, bar charts, annotations
• Log scale if range > 10×: Box plots, timing, any wide-range data
• Consistent colors: Same color = same method/category across all figures
• Axes labeled with SI units: Every axis has label + SI unit in parentheses (K, Pa, kg/m³, etc.)
• Grid lines: Dashed, alpha < 0.5, behind data
• No excessive whitespace: Use bbox_inches="tight" and compact figsize
• Legend readable: frameon=False, placed to minimize overlap with data
• 300 DPI minimum: Set in both rcParams and savefig
• Serif font: Times New Roman for Elsevier and most journals
• Inward tick marks: Cleaner look, standard for Elsevier
• Short IDs for many points: Use A1/B1/C1 with caption legend

Automated Validation

After generating all figures, run the figure validator:

python paperflow.py validate-figures papers/<paper_slug>/ --journal <journal_name>

This checks DPI, file format, minimum dimensions, and color mode against the journal profile. Fix all [!!] items before submission.

Alternative: Use figure_style.py Helper

Instead of manual rcParams setup, you can use the tools/figure_style.py module which wraps SciencePlots with journal presets:

from tools.figure_style import apply_style, save_fig, PALETTE, FIG_SINGLE

apply_style("elsevier")                    # or "ieee", "nature", "acs"
fig, ax = plt.subplots(figsize=FIG_SINGLE) # 3.5 × 2.8 inches
ax.plot(x, y, color=PALETTE[0])
save_fig(fig, "figures/fig01_results.png", dpi=300)

Common Mistakes Caught from CPA Paper

1. Rotated bar labels: Never rotate > 30°. Use short IDs instead.
2. Contour lines on noisy data: Creates ugly loops. Use pcolormesh.
3. Linear scale box plots with outliers: One 30× outlier squashes all other boxes to a 1-pixel line. Always use log scale for wide ranges.
4. Full system names as point labels: "Methane/Ethane/Propane/n-Butane" overlaps with neighbors. Use "B1" and define in table.
5. Large figure sizes: 10×8 inch figures waste journal space. Use 3.5×2.8 (single) or 7.0×3.5 (double column).
6. Inconsistent annotation offsets: When 4 points cluster at the same x-value, automated label placement fails. Use manual offsets dict.
7. Missing parity/reference lines: Always add y=1 line on speedup plots, parity line on comparison plots.

Conceptual / Architectural Diagrams

For framework papers, method papers, and system architecture descriptions, you need conceptual diagrams (layered architectures, workflow arrows, feedback loops) — not data plots. Use matplotlib.patches and matplotlib.text for full control over layout, styling, and publication quality.

Why matplotlib for conceptual diagrams?

• 300 DPI + PDF vector output — meets all journal requirements
• Exact font control — matches paper body (Times New Roman, 9pt)
• Reproducible — script regenerates identical figure after revisions
• No external tools — no Visio/PowerPoint/draw.io screenshots
• Consistent palette — same colors as data plots in the same paper

Pattern 7: Layered Architecture Diagram (Stacked Boxes)

Use for showing system layers, software stacks, or hierarchical structures.

import matplotlib.pyplot as plt
import matplotlib.patches as mpatches
from tools.figure_style import apply_style, save_fig, PALETTE, FIG_DOUBLE

apply_style("elsevier")

fig, ax = plt.subplots(figsize=FIG_DOUBLE)
ax.set_xlim(0, 10)
ax.set_ylim(0, 8)
ax.axis("off")

# Define layers bottom-to-top: (y_center, height, label, color)
layers = [
    (0.5, 0.8, "Layer 1: Foundation", PALETTE[0]),
    (1.5, 0.8, "Layer 2: Core", PALETTE[1]),
    (2.5, 0.8, "Layer 3: Services", PALETTE[2]),
    (3.5, 0.8, "Layer 4: Application", PALETTE[3]),
]

for y, h, label, color in layers:
    rect = mpatches.FancyBboxPatch(
        (1.0, y), 8.0, h,
        boxstyle="round,pad=0.1",
        facecolor=color, edgecolor="black", linewidth=0.6, alpha=0.25
    )
    ax.add_patch(rect)
    ax.text(5.0, y + h / 2, label, ha="center", va="center",
            fontsize=9, fontweight="bold")

# Add upward arrows between layers
for i in range(len(layers) - 1):
    y_from = layers[i][0] + layers[i][1]
    y_to = layers[i + 1][0]
    ax.annotate("", xy=(5.0, y_to), xytext=(5.0, y_from),
                arrowprops=dict(arrowstyle="->", color="black", lw=0.8))

save_fig(fig, "fig_architecture.png", dpi=300, formats=["pdf"])

Key rules for architecture diagrams:

• Use FancyBboxPatch with boxstyle="round,pad=0.1" for rounded corners
• Keep alpha=0.2–0.3 so text overlaid on boxes remains readable
• Use consistent left/right margin (x=1.0 to x=9.0 in a 0–10 coordinate space)
• Add description text in smaller font (7pt) below the layer label
• Arrows connect layers with annotate() using arrowstyle="->"

Pattern 8: Workflow / Pipeline Diagram (Horizontal Boxes + Arrows)

Use for showing sequential steps, pipelines, or phase progressions.

fig, ax = plt.subplots(figsize=FIG_DOUBLE)
ax.set_xlim(0, 14)
ax.set_ylim(0, 3)
ax.axis("off")

phases = ["Scope", "Research", "Analysis", "Validation", "Reporting"]
colors = [PALETTE[i] for i in range(len(phases))]
box_w, box_h = 2.0, 1.6
gap = 0.4
x_start = 0.5

for i, (phase, color) in enumerate(zip(phases, colors)):
    x = x_start + i * (box_w + gap)
    y = 0.7
    rect = mpatches.FancyBboxPatch(
        (x, y), box_w, box_h,
        boxstyle="round,pad=0.15",
        facecolor=color, edgecolor="black", linewidth=0.6, alpha=0.25
    )
    ax.add_patch(rect)
    ax.text(x + box_w / 2, y + box_h / 2 + 0.15, f"Phase {i+1}",
            ha="center", va="center", fontsize=7, color="grey")
    ax.text(x + box_w / 2, y + box_h / 2 - 0.15, phase,
            ha="center", va="center", fontsize=9, fontweight="bold")

    # Arrow to next box
    if i < len(phases) - 1:
        ax.annotate("", xy=(x + box_w + gap * 0.1, y + box_h / 2),
                    xytext=(x + box_w - 0.05, y + box_h / 2),
                    arrowprops=dict(arrowstyle="->", color="black", lw=0.8))

save_fig(fig, "fig_workflow.png", dpi=300, formats=["pdf"])

Pattern 9: Feedback Loop / Cycle Diagram

Use for digital twin loops, control loops, or iterative processes.

import numpy as np

fig, ax = plt.subplots(figsize=FIG_DOUBLE)
ax.set_xlim(-4, 4)
ax.set_ylim(-3, 3)
ax.set_aspect("equal")
ax.axis("off")

# Place nodes in a circle
labels = ["Plant", "Historian", "Agent", "Simulator", "Optimizer"]
n = len(labels)
radius = 2.2
angles = np.linspace(np.pi / 2, np.pi / 2 + 2 * np.pi, n, endpoint=False)

positions = [(radius * np.cos(a), radius * np.sin(a)) for a in angles]

for (x, y), label, color in zip(positions, labels, PALETTE):
    rect = mpatches.FancyBboxPatch(
        (x - 0.7, y - 0.35), 1.4, 0.7,
        boxstyle="round,pad=0.1",
        facecolor=color, alpha=0.25, edgecolor="black", linewidth=0.6
    )
    ax.add_patch(rect)
    ax.text(x, y, label, ha="center", va="center", fontsize=8, fontweight="bold")

# Draw curved arrows between consecutive nodes
for i in range(n):
    j = (i + 1) % n
    x1, y1 = positions[i]
    x2, y2 = positions[j]
    ax.annotate("", xy=(x2, y2), xytext=(x1, y1),
                arrowprops=dict(arrowstyle="->", color="black", lw=0.8,
                                connectionstyle="arc3,rad=0.15"))

save_fig(fig, "fig_loop.png", dpi=300, formats=["pdf"])

Pattern 10: Combined Mermaid + matplotlib

For rapid prototyping, use Mermaid for the initial layout concept, then implement the final version in matplotlib for publication quality.

Step 1 — Mermaid prototype (use renderMermaidDiagram tool in VS Code):

graph TD
    A[Plant Data] --> B[Agent]
    B --> C[Simulator]
    C --> D[Quality Gate]
    D --> E[Report]
    D -->|fail| B

Step 2 — Implement in matplotlib using Pattern 7/8/9 above.

• Mermaid rendered PNG is NOT suitable for journal submission (wrong fonts, cannot control DPI reliably, no serif fonts)
• Use it only as a visual guide for the matplotlib implementation

Checklist for Conceptual Diagrams

• Same font as paper body — serif (Times New Roman) via apply_style
• Color matches data figures — use same PALETTE throughout paper
• Low alpha on boxes (0.2–0.3) — text must be readable over fill
• Black thin borders — edgecolor="black", linewidth=0.6
• Rounded corners — boxstyle="round,pad=0.1" more professional
• Compact layout — use FIG_DOUBLE (7.0 × 3.5) max
• Short labels in diagram — long descriptions go in caption or paper text
• Arrows meaningful — every arrow represents a clear data flow or dependency
• Both PNG + PDF — save_fig(fig, name, formats=["pdf"])