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.