Custom Theme for Publication (thepubr)

The goal of thepubr is to custom theme, axis, font, size for publication output of ggplot2.

Installation

You can install the development version of thepubr like so:

devtools::install_github("haihuilab/thepubr")

Install fonts in Windows

We change the ggplot2 default Arial font to HelveticaNeueLTStd-Roman font. First, we install HelveticaNeueLTStd-Roman.ttf in windows or ubuntu from main folder.

Example

This is a basic example which shows you how to solve a common problem:

library(thepubr)
## basic example code
# Examples
library(ggplot2)
library(gridExtra)
library(tidyverse)

scatter <- ggplot(mtcars, aes(mpg,disp,color=factor(carb))) + geom_point(size=3, alpha = 0.7) + labs(title="Scatter Plot")
g1 <- grid.arrange(scatter,(scatter + scale_color_publication() + theme_publication()),nrow = 1)
# Small
save_figure(g1, filename = "example_plot_small", size = "small_wide")

g2 <- grid.arrange((scatter + scale_color_publication() + theme_publication(base_size = 24)),nrow = 1)
# Medium
save_figure(g2, filename = "example_plot_medium", size = "medium", device = "png")

bar <- ggplot(mtcars, aes(factor(carb),fill = factor(carb))) + geom_bar(alpha = 0.7) + labs(title = "Bar Plot")
# grid.arrange(bar,(bar + scale_color_publication(alpha = 0.8) + theme_publication()),nrow = 1)
g3 <- grid.arrange((bar + scale_color_publication() + theme_publication(base_size = 48)),nrow = 1)
# large
save_figure(g3, filename = "example_plot_large", size = "large")

What is special about using README.Rmd instead of just README.md? You can include R chunks like so:

summary(cars)
#>      speed           dist       
#>  Min.   : 4.0   Min.   :  2.00  
#>  1st Qu.:12.0   1st Qu.: 26.00  
#>  Median :15.0   Median : 36.00  
#>  Mean   :15.4   Mean   : 42.98  
#>  3rd Qu.:19.0   3rd Qu.: 56.00  
#>  Max.   :25.0   Max.   :120.00

You’ll still need to render README.Rmd regularly, to keep README.md up-to-date. devtools::build_readme() is handy for this. You could also use GitHub Actions to re-render README.Rmd every time you push. An example workflow can be found here: https://github.com/r-lib/actions/tree/v1/examples.

You can also embed plots, for example:

In that case, don’t forget to commit and push the resulting figure files, so they display on GitHub and CRAN.