Philosophy & Getting Started#

Start Early, Practice Often

• It’s never a bad time to generate clean, pretty figures

• Start learning early—it will pay off tremendously during manuscript preparation

• Sketch your figure layout on paper or digitally first

• Create a Sandbox file to experiment with new designs and variants

  • This can also be helpful when making multiple variants of a schematic for a talk or poster

• Typically easiest to import data as SVGs (vector format)

• Don’t stress about colors, line widths, or formatting in your raw plots (MATLAB, Python, etc.), it is more important to focus on the axes, try to make them as close to the “final” product as possible

  • For example, if your final plot is 0-20mm/s on y and 0-1s on x, try to have your MATLAB plot be the same rather than resizing

• Personal preference: embedding over dynamic links for stability

Ensuring Data Fidelity

• Keep all raw files together: Store traces, summary plots, and original exports in a dedicated folder
• Compare before finalizing: Always compare your figure-ready version with the original to ensure:
  • Axes scales and ranges remain accurate
  • Data points haven’t shifted during import/editing
  • Alignments match the original layout
  • No data has been accidentally deleted or modified
• Be critical when reviewing: Ask yourself, “Does what I’m plotting make sense?”
  • Do the axes ranges make biological/physical sense?
  • Are comparisons fair and appropriate?
  • Is the data representation honest and accurate?

Cleaning Up Imported Plots

1. Ungroup distinct elements (e.g., row 1 from row 2, data from axes)
2. May need to ungroup multiple times
3. Delete unnecessary background rectangles
4. Replace default fonts with consistent fonts
5. Fix any text that imported as outlines (may need to retype)
6. Simplify complex paths using Object → Path → Simplify

Version Control Strategies

• Use clear naming conventions: Fig1_v1.ai, Fig1_v2_revised.ai
• Save milestone versions before major changes

Toolkit Essentials#

Core Tools (Keyboard Shortcuts)

• Selection Tool (V) – Move and select objects
• Eyedropper Tool (I) – Sample and apply colors/styles
• Type Tool (T) – Add and edit text
• Line/Shape Tools – Create basic geometric elements
• Curvature Tool – Create smooth, clean paths for schematics
  • Use Smooth or Simplify features to improve imported paths

Essential Panels

• Align Panel – Precise spacing and alignment of elements
• Color Guide – Explore color variations and harmonies
• Swatches Panel – Save and manage color palettes

Key Operations

• Group / Ungroup (Ctrl/Cmd + G) – Keep subpanels organized and easy to move

• Clipping Mask (Make / Release) – Isolate regions without destructive editing

• Recolor Artwork – Apply new palettes across entire illustrations quickly

• Edit > Spelling > Check Spelling… – Spell check

File Organization#

Artboard Structure

• Treat each artboard as one complete figure (or major data group)
• Set artboard dimensions to match journal requirements
  • Can also ask a friend or lab member for examples if you are not sure where to start
• Name artboards clearly: “Figure 1”, “Supplementary 1”, “Behavior Data”, etc.
  • This will come in handy when exporting

Layer Organization

• Use top-level layers for each figure or major section (e.g., Fig 1, Fig 2, Sandbox, etc)
• Group subpanels (A, B, C…) to keep elements together and easy to move
• Lock or hide background layers to prevent accidental selection

Strategic Use of Layers vs. Groups

• Layers: Use for broad organization (different figures, experiment sections)
  • Provides high-level structure
  • Allows you to show/hide entire sections
  • Useful for managing complex multi-figure documents
• Groups: Use for flexible, day-to-day manipulation
  • Treat grouping as fluid—easily group and ungroup as needed
  • Group elements to quickly move them together
  • Ungroup to edit individual components

Practical Grouping Examples

• Group a schematic to move it to a new figure, then ungroup to edit it within that figure
• Group a data trace to “send it back” in the stacking order (Ctrl/Cmd + Shift + [), ensuring it appears behind axes
• Group all elements of panel A to move them as one unit, then ungroup to adjust spacing between elements
• Group related annotations (arrows, text, labels) to reposition them together
• Group legend components so they always move as a single unit

Here, I have set each layer to correspond to a Figure. I am interested in reorganizing the layout of Figure 6, so I have grouped each of the panels (e.g., B is highlighted) to make it easier to move them around.

Figure Formatting Standards#

Line Weights

• Axes line width: 0.5 pt
• Data line width: 1 pt
• Grid lines (if used): 0.25 pt

Typography

• Main text (axes labels, legends): 7 pt
• Minor text (annotations, statistics): 5 pt minimum
• Recommended font: Arial
• Use consistent capitalization (sentence case or title case)

Axis Consistency & Alignment#

Keep Axes Consistent

• Use the same tick direction, style, and scale across related plots
  • Example: brackets with ticks facing the data, 0.02 in wide for every plot
• Match axis ranges when comparing similar data
• Keep tick mark spacing proportional to data range

Alignment Across Panels (Rows & Columns)

• Align subpanels whenever possible—both vertically and horizontally

• Ideally align by:

  • Axes positions
  • Axis labels (especially Y-axis labels)
  • Panel letters

• Can also align using visual features like diagram edges or arrows

• Use Illustrator’s Smart Guides (Ctrl/Cmd + U) to help with alignment

Panel Size & Proportion

• For repeated plot types, keep identical dimensions
• If sizes differ, make proportions intentional and consistent
  • Example: a feature panel is exactly ½ the height of the adjacent plot
• Choose complementary dimensions that minimize empty space

Here, notice how the schematic in A fits to the same vertical dimensions as the example traces to the right (blue). Or how the summary plots in C is 2 panels high but occupies the same vertical space as the plots in B which is 3 panels high.

Also, notice how the text and axes in B and D are aligned. The end of B on the right also corresponds with the end of E on the right, allowing the axes in C and F to also align.

While it might seem like overkill (it probably is), I would argue that making figures easier to visually digest makes them more compelling and makes your data stand out better to folks that are visual learners.

Color Strategy#

Color Palette Philosophy

• Avoid color where possible—more colors add visual clutter
• Use color purposefully to highlight specific data or comparisons
• Build contrast by pairing warm against cool tones
  • For example, in my figures I use a cool blue and purple, and will highlight with a warm pink
• Choose your base colors first, then worry about accents

Color Palette Resources

• Try Coolors to explore palette ideas: https://coolors.co/
• Consider colorblind-friendly palettes (avoid red-green combinations)
• Use ColorBrewer for cartography-inspired scientific palettes
• Test palettes using colorblind simulators online

Choosing & Refining Colors

• Color Guide Panel:
  • Adjust current color hue, shade, tint
  • Find complementary or analogous color schemes

• Swatches Panel:
  • Save color palettes for easy reuse across figures
  • Create organized swatch groups for different data categories

• Recolor Artwork:
  • Apply new palettes across entire illustrations
  • Quickly iterate on design directions
  • Easily catch and fix tiny color inconsistencies

Here, I can use the Recolor tool to apply a new swatch of colors to this figure. I could change one color (e.g., if I decide I want a different shade of blue) by changing the color in the New column or by adjusting the color/brightness/contrast sliders.

Or I could change the entire color palette by switching to a new Swatch group. For instance, if I have a figure where I like the color scheme, I could save those colors as a Swatch and apply them to a different figure to make them match.

You can also use the Color Libraries to select a new color palette based on pre-saved libraries.

Common Pitfalls to Avoid#

Layout Issues

• Overlapping text or crowded labels—give elements breathing room
• Inconsistent spacing between panels—use Align panel for precision
• Misaligned elements across panels—use guides and Smart Guides
• Panel labels in inconsistent positions

Styling Problems

• Using default chart colors without consideration
• Mixing different fonts or font sizes inconsistently
• Varying line weights for the same element type
• Overuse of effects (shadows, glows, gradients)

Exporting Figures#

Export Options

• Export Selection: For single panels or insets (File → Export Selection)
• Export Artboards: Batch-export all or selected figures (File → Export → Export for Screens)
  • Export at 1200 ppi for high resolution

📎 Figures_v4.ai