Creating figures

Nature's recommendations

• Figure size (canvas/artboard size in Illustrator / Affinity Designer / Inkscape):
  • Full column: 183 mm (7.2 in)
  • Half column: 89 mm (3.5 in)
  • 1.5 column: 120 mm (4.72 in) or 136 mm (5.35 in)
  • Maximal height: 247 mm (9.72 in)
  • DPI: At least 300, but 450 recommended (>450 dpi will be downsampled to 450 dpi)
• Images:
  • Resolution: Same as figure DPI
  • Color space: RGB
• Text:
  • Regular text: Sans-serif (Arial, Helvetica)
  • Amino-acid sequences: Monospace (Courier New), 50 or 100 characters per line
  • Glyphs and greek characters: Symbol font
  • Size: 5-7 pt for regular text, 8 pt bold for panel labels (a, b, c, ...)
  • Axes labelled with text and units in parentheses (e.g., Data (unit))
  • Avoid colored text, preferring colored boxes in the legend
  • Keep axis lines and tick marks
  • Avoid decorative elements (shadows, icons, gridlines)
• Colors:
  • Use contrasting colors to aid color blind individuals (Matplotlib's default categorical colormap tab10 is colorblind-safe)
  • Use solid colors to fill shapes, not patterns
• Saving:
  • .pdf or .eps
  • Do not convert text to raster or outlines
  • Embed fonts (TrueType 2 or 42)
  • Same as figure DPI

Example code

import io, re
import matplotlib.pyplot as plt
import pyperclip


plt.rcParams['font.family'] = 'sans-serif'
plt.rcParams['font.sans-serif'] = ['Arial']
plt.rcParams['pdf.fonttype'] = 42
plt.rcParams['svg.fonttype'] = 'none'
plt.rcParams['font.size'] = 6
plt.rcParams['axes.titlesize'] = 7
plt.rcParams['figure.titlesize'] = 7


def copy_and_show_fig(fig, dpi=450):
    """Copies SVG to clipboard and displays figure
    """
    buf = io.StringIO()
    fig.patch.set_visible(False)   # remove the global background patch
    for ax in fig.axes:
        ax.patch.set_visible(False)  # remove each Axes background patch
    fig.savefig(buf, format='svg', transparent=True, bbox_inches='tight', pad_inches=0)
    svg_data = buf.getvalue()

    # patch width/height from pt to px
    m = re.search(r'viewBox="\s*([-\d.]+)\s+([-\d.]+)\s+([-\d.]+)\s+([-\d.]+)"', svg_data)
    w_pt, h_pt = float(m.group(3)), float(m.group(4))
    w_px = int(round(w_pt * dpi / 72))
    h_px = int(round(h_pt * dpi / 72))

    svg_data = re.sub(r'(<svg[^>]*?)width="[^"]+"', rf'\1width="{w_px}px"', svg_data, count=1)
    svg_data = re.sub(r'(<svg[^>]*?)height="[^"]+"', rf'\1height="{h_px}px"', svg_data, count=1)
    pyperclip.copy(svg_data)

    fig.set_dpi(200)
    fig.patch.set_visible(True)


fig, ax = plt.subplots(figsize=(3.5, 2.33))  # Corresponds to 183 mm width

# This is a simple example
y = range(1, 10)
x = range(len(y))
ax.bar(x, y)
ax.set_title('A simple bar plot')
ax.set_xlabel('Item ID')
ax.set_ylabel('Number of items')
ax.spines['right'].set_visible(False)
ax.spines['top'].set_visible(False)

# Draw your figure and copy SVG to clipboard
copy_and_show_fig(fig)