In csdaw/ggprism: A 'ggplot2' Extension Inspired by 'GraphPad Prism'

knitr::opts_chunk$set(
  echo = FALSE,
  collapse = TRUE,
  comment = "#>",
  dpi = 120,
  fig.width = 6,
  out.width = 400,
  fig.path = "man/figures/README-"
)

library(ggplot2)
library(dplyr)
library(tidyr)
library(ggprism)
library(ggnewscale)

ggprism

The ggprism package provides various themes, palettes, and other useful functions to customise ggplots and give them the 'GraphPad Prism' look.

Install

Install the latest version from CRAN:

install.packages("ggprism")

Install the development version from GitHub:

remotes::install_github("csdaw/ggprism")

How to Use

See the Getting Started page for a quick overview of ggprism features. Detailed examples and instructions can be found below and on the ggprism website.

library(ggplot2)
library(ggprism)

tg <- ToothGrowth
tg$dose <- as.factor(tg$dose)

base <- ggplot(tg, aes(x = dose, y = len)) + 
  geom_violin(aes(colour = dose, fill = dose), trim = FALSE) + 
  geom_boxplot(aes(fill = dose), width = 0.2, colour = "black") + 
  scale_y_continuous(limits = c(-5, 40))

p_vals <- tibble::tribble(
  ~group1, ~group2, ~p.adj,   ~y.position,
  "0.5",   "1",     8.80e-14, 35,
  "0.5",   "2",     1.27e-7,  39
)

base

base + 
  scale_color_prism("floral") + 
  scale_fill_prism("floral") + 
  guides(y = "prism_offset_minor") + 
  theme_prism(base_size = 16) + 
  theme(legend.position = "none") + 
  add_pvalue(p_vals, label = "p = {p.adj}", tip.length = 0, label.size = 4)

Feedback and Contributions

Any feedback, questions, and suggestions are welcome and should be shared via GitHub discussions.

Bug reports should be submitted via GitHub issues with a minimal reproducible example, e.g. using the reprex package.

Contributions to ggprism are also welcome and pull requires should also be submitted via GitHub issues. Please fork/clone this repository and create a new branch to develop your contribution in. Some ways to contribute might include:

Updates and corrections to documentation
Examples and vignettes for existing functions
Bug fixes
New functions with associated documentation, examples, and tests

Cite

I would be very grateful if you could cite this package if you use it in your publication:

Charlotte Dawson (r format(Sys.Date(), "%Y")). ggprism: A 'ggplot2' Extension Inspired by 'GraphPad Prism'. R package version r getNamespaceVersion("ggprism"). https://cran.r-project.org/package=ggprism doi: 10.5281/zenodo.4556067

# BibTex for LaTeX users
@Manual{
title = {ggprism: A 'ggplot2' Extension Inspired by 'GraphPad Prism'},
author = {Charlotte Dawson},
year = {`r format(Sys.Date(), "%Y")`},
note = {R package version `r getNamespaceVersion("ggprism")`},
url = {https://cran.r-project.org/package=ggprism},
doi = {10.5281/zenodo.4556067}
}

More Examples

Recreates this figure from the GraphPad Prism website. See this vignette for the source code and step-by-step instructions.

df <- data.frame(
  agonist = c(1e-10, 1e-8, 3e-8, 1e-7, 3e-7, 1e-6, 3e-6, 1e-5, 3e-5, 1e-4, 3e-4),
  ctr1 = c(0, 11, 125, 190, 258, 322, 354, 348, NA, 412, NA),
  ctr2 = c(3, 33, 141, 218, 289, 353, 359, 298, NA, 378, NA),
  ctr3 = c(2, 25, 160, 196, 345, 328, 369, 372, NA, 399, NA),
  trt1 = c(3, NA, 11, 52, 80, 171, 289, 272, 359, 352, 389),
  trt2 = c(5, NA, 25, 55, 77, 195, 230, 333, 306, 320, 338), 
  trt3 = c(4, NA, 28, 61, 44, 246, 243, 310, 297, 365, NA)
) %>% 
  mutate(log.agonist = log10(agonist)) %>% 
  pivot_longer(
    c(-agonist, -log.agonist), 
    names_pattern = "(.{3})([0-9])", names_to = c("treatment", "rep")
  ) %>% 
  filter(!is.na(value))

dr_eq <- y ~ min + ((max - min) / (1 + 10^(ec50 - (x))))

# Before
ggplot(df, aes(x = log.agonist, y = value, colour = treatment, shape = treatment)) + 
  geom_point() + 
  geom_smooth(method = "nls", formula = dr_eq, se = FALSE,
              method.args = list(start = list(min = 1.67, max = 397, ec50 = -7))) + 
  scale_x_continuous(
    limits = c(-10, -3), breaks = -10:-3,
    minor_breaks = log10(rep(1:9, 7)*(10^rep(-10:-4, each = 9)))
  ) + 
  scale_y_continuous(limits = c(-100, 500), breaks = seq(-100, 500, 100)) + 
  theme_grey(base_size = 11) +
  scale_colour_discrete(labels = c("No inhibitor", "Inhibitor")) + 
  scale_shape_discrete(labels = c("No inhibitor", "Inhibitor")) +
  guides(colour = guide_legend(position = "inside"),
         shape = guide_legend(position = "inside")) +
  theme(axis.title.y = element_blank(),
        legend.title = element_blank(),
        legend.position.inside = c(0.05, 0.95),
        legend.justification = c(0.05, 0.95)) + 
  labs(x = "[Agonist], M")

# After
exp_bold <- function(lab) {
  do.call(
    expression,
    lapply(paste(lab), function(x) bquote(bold("10"^.(x))))
  )
}

ggplot(df, aes(x = log.agonist, y = value, shape = treatment)) + 
  geom_smooth(aes(colour = treatment),
              method = "nls", formula = dr_eq, se = FALSE,
              method.args = list(start = list(min = 1.67, max = 397, ec50 = -7))) + 
  scale_colour_manual(labels = c("No inhibitor", "Inhibitor"),
                      values = c("#00167B", "#9FA3FE")) +
  scale_x_continuous(
    limits = c(-10, -3), breaks = -10:-3,
    minor_breaks = log10(rep(1:9, 7)*(10^rep(-10:-4, each = 9))),
    labels = exp_bold,
    guide = "prism_offset_minor"
  ) + 
  scale_y_continuous(
    limits = c(-100, 500), breaks = seq(-100, 500, 100),
    guide = "prism_offset"
  ) + 
  guides(colour = guide_legend(position = "inside"),
         shape = guide_legend(position = "inside")) +
  theme(legend.title = element_blank(),
        legend.position.inside = c(0.05, 0.95),
        legend.justification = c(0.05, 0.95)) +
  new_scale_colour() + 
  geom_point(aes(colour = treatment), size = 3) + 
  theme_prism("winter_bright", base_size = 16) + 
  theme(legend.title = element_blank(),
        legend.position.inside = c(0.05, 0.95),
        legend.justification = c(0.05, 0.95)) +
  scale_colour_prism("winter_bright", labels = c("No inhibitor", "Inhibitor")) + 
  scale_shape_prism(labels = c("No inhibitor", "Inhibitor")) + 
  theme(axis.title.y = element_blank()) + 
  labs(x = "[Agonist], M")

Recreates Figure 2B from Matsushita & Nishimura (2020), which was originally created using GraphPad Prism. See this vignette for the source code and step-by-step instructions.

df2 <- wings %>%
  mutate(measure = stringr::str_to_title(measure))

wings.pvals <- df2 %>%
  group_by(sex, measure) %>%
  rstatix::t_test(percent.change ~ genotype, p.adjust.method = "BH", var.equal = TRUE, ref.group = "Tps1MIC/+") %>%
  rstatix::add_x_position(x = "measure", dodge = 0.9) %>%
  mutate(label = c("***", "*", "P = 0.26", "***", "***", "P = 0.65"))

# Before
ggplot(df2, aes(
  x = factor(measure, levels = c("Wing.size", "Cell.size", "Cell.number")),
  y = percent.change)
) +
  ggbeeswarm::geom_beeswarm(
    aes(fill = genotype),
    dodge.width = 0.9, 
    #spacing = 1.6, 
    shape = 21
  ) +
  scale_y_continuous(
    limits = c(-20, 12),
    expand = c(0, 0),
    breaks = seq(-20, 10, 5)
  ) +
  scale_x_discrete(
    labels = function(x) stringr::str_wrap(gsub("\\.", " ", x), width = 5)
  ) +
  facet_wrap(
    ~ sex, 
    scales = "free",
    labeller = labeller(sex = c(male = "\u2642", female = "\u2640"))
  ) +
  scale_fill_manual(
    values = c("#026FEE", "#87FFFF"), 
    labels = c(expression("Tps"*1^italic("MIC")~"/ +"), expression("Tps"*1^italic("MIC")))
  ) +
  labs(y = "% change") +
  theme(
    legend.position = "bottom",
    axis.title.x = element_blank(),
    strip.text = element_text(size = 14),
    legend.spacing.x = unit(0, "pt"),
    legend.text = element_text(margin = margin(r = 20))
  ) +
  geom_hline(yintercept = 0, linetype = 2, linewidth = 0.3) +
  stat_summary(
    geom = "crossbar",
    aes(fill = genotype),
    fun = mean,
    position = position_dodge(0.9),
    colour = "red",
    linewidth = 0.4, width = 0.7,
    show.legend = FALSE
  ) +
  geom_text(
    data = data.frame(
      sex = factor("female", levels = c("male", "female")), 
      measure = "Cell.number", 
      percent.change = -18.5, 
      lab = "(n = 10)"
    ), 
    aes(label = lab)
  ) +
  guides(fill = guide_legend(override.aes = list(size=3)))

# After
ggplot(df2, aes(
  x = factor(measure, levels = c("Wing.size", "Cell.size", "Cell.number")),
  y = percent.change)
) +
  ggbeeswarm::geom_beeswarm(
    aes(fill = genotype),
    dodge.width = 0.9, 
    #spacing = 1.6, 
    shape = 21
  ) +
  scale_y_continuous(
    limits = c(-20, 12),
    expand = c(0, 0),
    breaks = seq(-20, 10, 5),
    guide = "prism_offset"
  ) +
  scale_x_discrete(
    guide = guide_prism_bracket(width = 0.15), 
    labels = function(x) stringr::str_wrap(gsub("\\.", " ", x), width = 5)
  ) +
  facet_wrap(
    ~ sex, 
    scales = "free",
    labeller = labeller(sex = c(male = "\u2642", female = "\u2640"))
  ) +
  theme_prism(base_fontface = "plain", base_line_size = 0.7, base_family = "Arial") +
  scale_fill_manual(
    values = c("#026FEE", "#87FFFF"), 
    labels = c(expression("Tps"*1^italic("MIC")~"/ +"), expression("Tps"*1^italic("MIC")))
  ) +
  labs(y = "% change") +
  theme(
    legend.position = "bottom",
    axis.title.x = element_blank(),
    strip.text = element_text(size = 14),
    legend.spacing.x = unit(0, "pt"),
    legend.text = element_text(margin = margin(r = 20))
  ) +
  geom_hline(yintercept = 0, linetype = 2, linewidth = 0.3) +
  stat_summary(
    geom = "crossbar",
    aes(fill = genotype),
    fun = mean,
    position = position_dodge(0.9),
    colour = "red",
    linewidth = 0.4, width = 0.7,
    show.legend = FALSE
  ) +
  add_pvalue(
    wings.pvals, y = 10, xmin = "xmin", xmax = "xmax", tip.length = 0, 
    fontface = "italic", lineend = "round", bracket.size = 0.5
  ) +
  geom_text(
    data = data.frame(
      sex = factor("female", levels = c("male", "female")), 
      measure = "Cell.number", 
      percent.change = -18.5, 
      lab = "(n = 10)"
    ), 
    aes(label = lab)
  ) +
  guides(fill = guide_legend(override.aes = list(size=3)))