bio-reporting-figure-export

by FreedomIntelligence

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SKILL.md About

<!--
# COPYRIGHT NOTICE
# This file is part of the "Universal Biomedical Skills" project.
# Copyright (c) 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu>
# All Rights Reserved.
#
# This code is proprietary and confidential.
# Unauthorized copying of this file, via any medium is strictly prohibited.
#
# Provenance: Authenticated by MD BABU MIA

-->

---
name: bio-reporting-figure-export
description: Exports publication-ready figures in various formats with proper resolution, sizing, and typography. Use when preparing figures for journal submission, creating vector graphics for presentations, or ensuring consistent figure styling across analyses.
tool_type: mixed
primary_tool: matplotlib
measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes.
allowed-tools:
  - read_file
  - run_shell_command
---

# Publication-Ready Figure Export

## Python (matplotlib)

```python
import matplotlib.pyplot as plt

# Set publication defaults
plt.rcParams.update({
    'font.size': 8,
    'font.family': 'Arial',
    'axes.linewidth': 0.5,
    'lines.linewidth': 1,
    'figure.dpi': 300
})

fig, ax = plt.subplots(figsize=(3.5, 3))  # Single column width
# ... create plot ...

# Save in multiple formats
fig.savefig('figure1.pdf', bbox_inches='tight', dpi=300)
fig.savefig('figure1.png', bbox_inches='tight', dpi=300)
fig.savefig('figure1.svg', bbox_inches='tight')
```

## R (ggplot2)

```r
library(ggplot2)

p <- ggplot(data, aes(x, y)) + geom_point() +
  theme_classic(base_size = 8) +
  theme(text = element_text(family = 'Arial'))

# PDF for vector graphics
ggsave('figure1.pdf', p, width = 3.5, height = 3, units = 'in')

# High-res PNG
ggsave('figure1.png', p, width = 3.5, height = 3, units = 'in', dpi = 300)

# TIFF (some journals require)
ggsave('figure1.tiff', p, width = 3.5, height = 3, units = 'in',
       dpi = 300, compression = 'lzw')
```

## Journal Requirements

| Journal Type | Format | Resolution | Width |
|--------------|--------|------------|-------|
| Most journals | PDF/EPS | Vector | 3.5" (1-col), 7" (2-col) |
| Online-only | PNG | 300 DPI | Variable |
| Print | TIFF | 300-600 DPI | Column width |

## Multi-panel Figures

```python
import matplotlib.pyplot as plt
from matplotlib.gridspec import GridSpec

fig = plt.figure(figsize=(7, 5))  # Two-column width
gs = GridSpec(2, 3, figure=fig)

ax1 = fig.add_subplot(gs[0, 0])
ax2 = fig.add_subplot(gs[0, 1:])
ax3 = fig.add_subplot(gs[1, :])

# Add panel labels
for ax, label in zip([ax1, ax2, ax3], ['A', 'B', 'C']):
    ax.text(-0.1, 1.1, label, transform=ax.transAxes,
            fontsize=10, fontweight='bold')

fig.savefig('figure_multipanel.pdf', bbox_inches='tight')
```

## Color Considerations

- Use colorblind-friendly palettes (viridis, cividis)
- Ensure sufficient contrast for grayscale printing
- Maintain consistency across all figures

## Related Skills

- data-visualization/ggplot2-fundamentals - Creating plots in R
- data-visualization/heatmaps-clustering - Complex visualizations
- data-visualization/multipanel-figures - Figure composition