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https://csdaw.github.io/ggprism/
ggplot2 extension inspired by GraphPad Prism
https://csdaw.github.io/ggprism/
ggplot-extension ggplot2 prism r
Last synced: about 2 months ago
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ggplot2 extension inspired by GraphPad Prism
- Host: GitHub
- URL: https://csdaw.github.io/ggprism/
- Owner: csdaw
- Created: 2020-03-29T14:59:24.000Z (over 4 years ago)
- Default Branch: master
- Last Pushed: 2024-03-21T10:11:20.000Z (6 months ago)
- Last Synced: 2024-04-25T08:21:06.378Z (5 months ago)
- Topics: ggplot-extension, ggplot2, prism, r
- Language: R
- Homepage: https://csdaw.github.io/ggprism/
- Size: 94.1 MB
- Stars: 161
- Watchers: 6
- Forks: 21
- Open Issues: 8
-
Metadata Files:
- Readme: README.Rmd
Awesome Lists containing this project
README
---
output: github_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(
echo = FALSE,
collapse = TRUE,
comment = "#>",
dpi = 120,
fig.width = 6,
out.width = 400,
fig.path = "man/figures/README-"
)
library(ggplot2)
library(dplyr)
library(tidyr)
library(ggprism)
library(ggnewscale)
```
# ggprism 
[](https://github.com/csdaw/ggprism/actions/workflows/R-CMD-check.yaml)
[](https://app.codecov.io/gh/csdaw/ggprism?branch=master)
[](https://cran.r-project.org/package=ggprism)
[](https://csdaw.github.io/ggprism/)
[](https://zenodo.org/badge/latestdoi/251058802)
The `ggprism` package provides various themes, palettes, and other useful
functions to customise ggplots and give them the _'GraphPad Prism'_ look.
## Install
Install the latest version from CRAN:
```{r, eval=FALSE, echo=TRUE}
install.packages("ggprism")
```
Install the development version from GitHub:
```{r, eval=FALSE, echo=TRUE}
remotes::install_github("csdaw/ggprism")
```
## How to Use
See the [Getting Started](https://csdaw.github.io/ggprism/articles/ggprism.html)
page for a quick overview of `ggprism` features.
Detailed examples and instructions can be found below and on the
[`ggprism` website](https://csdaw.github.io/ggprism/).
```{r, echo=TRUE}
library(ggplot2)
library(ggprism)
tg <- ToothGrowth
tg$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
)
```
```{r ex, echo=TRUE, fig.show='hold'}
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](https://github.com/csdaw/ggprism/discussions).
Bug reports should be submitted via
[GitHub issues](https://github.com/csdaw/ggprism/issues)
with a minimal reproducible example, e.g. using the
[`reprex`](https://reprex.tidyverse.org) package.
Contributions to `ggprism` are also welcome and pull requires should also be
submitted via [GitHub issues](https://github.com/csdaw/ggprism/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")`.
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](https://cdn.graphpad.com/assets/0.27.0/images/srcset/prism-get-actionable-help-w1920-800.png)
from the GraphPad Prism website. See
[this vignette](https://csdaw.github.io/ggprism/articles/web-only/ex1-dose.html) for the
source code and step-by-step instructions.
```{r}
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))))
```
```{r ex2, warning=FALSE}
# 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)](https://doi.org/10.1038/s42003-020-0889-1),
which was originally created using GraphPad Prism. See
[this vignette](https://csdaw.github.io/ggprism/articles/web-only/ex2-wings.html) for the
source code and step-by-step instructions.
```{r}
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"))
```
```{r ex3}
# 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)))
```