My template for controlling publication quality figures

January 28, 2013
By

(This article was first published on me nugget, and kindly contributed to R-bloggers)



The following is a template that I usually start with when producing figures for publication. It allows me to control:
  1. The overall size of the figure (in inches) (WIDTH, HEIGHT)
  2. The layout of figure subplots (using the layout() function) (LO)
  3. The resolution of the figure (for a .png file) (RESO)
I define the overall dimensions of the figure in units of measurement (e.g. inches or centimeters) in order to control how the figure will look on the printed page. For example, a typical journal page might have ~8 inches of space for a 2 column figure and ~4 inches for a 1 column figure.

I define margins (mar, oma) in terms of point size (ps), since this relates to the height of text, which allows of control of axis labeling. By defining the outer margins (OMA) and point size (PS) before calling layout, you will have these margins incorporated. Then, by running the x11() device (after the #), you can check your figure layout with layout.show(n):

 

I learned recently that the layout() function will adjust the character expansion size (par()$cex) depending on how your device is split up. For that reason, I usually include another line of code resetting par(cex=1) before proceeding with individual plots.

Finally, the three different device types included in the template are:
  1. x11(), for initial tweaking of the layout and general functionality of the plotting code
  2. png(), for producing a compact figure useful in pasting into Word documents, and for cases where the figure contains a lot of information and would be slow to loading as a .pdf
  3. pdf(), for a vector-based figure that is fully scalable / zoomable. When not too big, these figures look the best, and can also be embedded in LaTeX documents
I have been able to use this template to successfully control my figures to the formatting requirements of specific journals or other publications (e.g. overall size, point size, resolution, etc.).


Figure template:
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