Examples of Plots for Manuscripts

We provide examples of plots in R for publications.

There are many online tutorials and resources for plotting and dataframe manipulation in R. Here, instead, we provide examples and tips for generating plots in R for manuscripts or presentations.

Contents

• Line plots
  • Line plot with error bars
• Scatter plots
  • Scatter Plot with bins

Prerequisites

Basic knowledge of the following are assumed.

• R
• ggplot
• dplyr

General Guidelines

• Use ggplot instead of R's built-in plotting functions.
• Have your plot saved in an object in your script. You may need to combine it with other plots later.
• Save your plot in PDF format. Vector graphics formats, such as PDF, are higly preferred to pixel-based formats such as jpeg and png.
• Once you agree on the colors and the general outlook, decide on the dimensions of your plot. Then, work your way backwards. Save your plot in a PDF file. View this file to fine-tune your plot. You may need to do this in many iterations.
• When you decide to finalize your figures, print them in 100% scale. Make sure they look good on paper too.
• Have your plotting parameters (axis thickness, font size, etc.) saved in variables in one place. Use these variables throughout your project. This way, you can manage a manuscript with many figures easily and consistently.
• Have a color scheme and use these colors consistently. For example, use the same shades of blue for control experiments and the same shades of orange for treatment experiments.