Barrick Lab Style Guide for Figures

General Workflow

• Use a program (Excel, R, CIRCOS, matplotlib, etc.) to graph your data.
• Output a file in a vector graphics file format (SVG or PDF).
• Integrate the graphs into an annotated figure in Adobe Illustrator.

As an example...

Things to do in Excel before exporting

• Change the font of all labels to Arial or Helvetica
• Resize symbols and fonts so that they look good in proportion.
• Remove all grid lines.
• Outline the graph area with a box.
• Change all line widths (axes, box) to 1 point.
• Remove the border around the whole graph area.
• Remove all shadow effects.

This is a figure created in Microsoft Excel of two sets of fitness measurements.

This is the final figure created by importing this graph into Adobe Illustrator. Notice:

• The line widths of error bars and ticks have been further adjusted for better visibility.
• Shadow effects have been removed.
• The legend has been expanded.
• Horizontal lines showing the averages of each time series have been added.
• The names have been changed from abstruse strain numbers into simple numbering.
• A panel describing the overall experiment has been added.

General Guidelines for Figures

• Fonts
  • Always use Arial (or Helvetica).
  • Avoid font sizes smaller than 6 pts as much as possible.
  • Generally label figure subparts with capital bold letters of 12-14 pt size.
• Use CMYK color. This is what journals use for print copies.
  • Blues, in particular, look much different than in RGB space.
• Generally, DO NOT use:
  • Shadows, halos, etc., or other shading effects. Be aware that this is the default in many Microsoft programs.
  • Cross-hashing. There can be odd effects when printing close cross-hashes.
  • More than one kind of dashed line.

What type of graph should I use for my data?

• Types of data
  • Relative fitness
  • Expression levels
  • Mutation rates

• Don't use bar graphs when a log scale is the natural scale.

What type of error bars should I use for my data?

• See this helpful article for differences between standard deviation, standard error, and confidence intervals:
  • Cumming G, Fidler F, Vaux DL. 2007. Error bars in experimental biology. J. Cell Biol. 177:7–11. «PubMed»
• Use 95% confidence intervals when comparing sets of measurements on a graph (e.g., fitness values).
• Use standard deviations when graphing values where you merely want to show the range of values observed across several replicates (e.g., OD values at one point on a growth curve).

Using Excel to Create Graphs

• Differences from Excel defaults
  • Remove black box from the outside of the graph.
  • Remove horizontal dividing lines.
  • Outline graph area and make axes use 1 pt black lines.
• Change the default font to Arial or Helvetica before exporting. Other fonts (including the Calibri default!) can change into random symbols when loading into Illustrator.

Creating Figures in Adobe Illustrator

• Imported graphs.
  • Be careful to only perform isomorphic transformations on imported graphs. Obviously it is important to preserve the exact locations of ticks relative to data.
  • Since you can determine the exact pixel locations of what you draw in Adobe Illustrator, you can calculate exactly where to place extra features in the context of your graph.