Opinionated Themes for Scientific Reports • pmthemes

This is a small package containing functions for producing consistent documents and figures for scientific reports.

Installation

You can install pmthemes() from github with:

# install.packages("devtools")
devtools::install_github("petermacp/pmthemes")

Overall theme

The theme_pm() function is the workhorse of the package, providing a simple theme for scientific presentations and documents.

library(ggplot2)
library(palmerpenguins)
library(pmthemes)

ggplot(data = penguins, aes(x = flipper_length_mm, y = body_mass_g)) +
  geom_point(aes(color = species,
                 shape = species),
             size = 2) +
  facet_grid(~species) +
  scale_color_manual(values = c("darkorange","darkorchid","cyan4"))  +
  labs(title = "This is a test graph",
       subtitle = "Showing theme_pm()",
       caption = "Data from the palmerpenguins package") +
  theme_pm()
#> Warning: Removed 2 rows containing missing values (geom_point).

Vintage rail poster colour themes

The scale_colour_rail() and scale_fill_rail() functions are used to define colour palettes for aesthetics specified in the scale name.

Much of the code for extracting colour palettes from images using a k-means clustering images was taken from: http://www.milanor.net/blog/build-color-palette-from-image-with-paletter/

There are seven different palettes, each based on a vintage British railway poster:

aberdeen

cornwall

harrogate

penzance

somerset

wales

yorkshirecoast

Examples

An example using the cornwall palette.

library(ggplot2)
library(pmthemes)

ggplot(data = diamonds) +
  geom_bar(aes(x = cut, fill = cut)) +
  theme_pm() +
  scale_fill_rail(palette="cornwall")

Here is the harrogate palette.

library(ggplot2)
library(pmthemes)

ggplot(data = diamonds) +
  geom_bar(mapping = aes(x = cut, fill = cut)) +
  theme_pm() +
  scale_fill_rail(palette="harrogate")

…and the penzance palette.

ggplot(data = diamonds) +
  geom_bar(mapping = aes(x = cut, fill = cut)) +
  theme_pm() +
  scale_fill_rail(palette="penzance")

R Markdown template

The pmthemes package will additionally install an R Markdown template for writing scientific analysis report.

To use the package, run: library(pmthemes), then File/New File/R Markdown/From template. Then click on the Analysis template file to open a new R Markdown document.

You will need to modify the yaml header to provide your own information.

pmthemes