README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include=FALSE}
knitr::knit_hooks$set(pngquant = knitr::hook_pngquant)

knitr::opts_chunk$set(
  echo = FALSE,
  message = FALSE,
  fig.path = "man/figures/README-",
  collapse = TRUE,
  comment = "#>",
  dev = "ragg_png",
  dpi = 72,
  fig.retina = 2,
  fig.width = 10.6667,
  fig.height = 3.3334,
  fig.align = "center",
  out.width = "100%",
  pngquant = "--speed=1 --quality=50"
)
```

# ggsci <img src="man/figures/logo.png" align="right" width="120" />

<!-- badges: start -->
[![R-CMD-check](https://github.com/nanxstats/ggsci/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/nanxstats/ggsci/actions/workflows/R-CMD-check.yaml)
[![CRAN Version](https://www.r-pkg.org/badges/version/ggsci)](https://cran.r-project.org/package=ggsci)
[![Downloads from the RStudio CRAN mirror](https://cranlogs.r-pkg.org/badges/ggsci)](https://cran.r-project.org/package=ggsci)
<!-- badges: end -->

`ggsci` offers a collection of `ggplot2` color palettes inspired by
scientific journals, data visualization libraries, science fiction movies,
and TV shows.

## Installation

You can install `ggsci` from CRAN:

```r
install.packages("ggsci")
```

Or try the development version on GitHub:

```r
remotes::install_github("nanxstats/ggsci")
```

[Browse the vignette](https://nanx.me/ggsci/articles/ggsci.html) (or open with
`vignette("ggsci")` in R) for a quick-start guide.

## Gallery

```{r}
library("ggsci")
library("ggplot2")
library("gridExtra")

data("diamonds")

p1 <- ggplot(
  subset(diamonds, carat >= 2.2),
  aes(x = table, y = price, colour = cut)
) +
  geom_point(alpha = 0.7) +
  geom_smooth(method = "loess", alpha = 0.05, linewidth = 1, span = 1) +
  theme_bw() +
  theme(
    axis.title.x = element_blank(),
    axis.title.y = element_blank()
  )

p2 <- ggplot(
  subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
  aes(x = depth, fill = cut)
) +
  geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
  theme_bw() +
  theme(
    axis.title.x = element_blank(),
    axis.title.y = element_blank()
  )
```

### NPG

```{r, ggsci-npg}
p1_npg <- p1 + scale_color_npg()
p2_npg <- p2 + scale_fill_npg()
grid.arrange(p1_npg, p2_npg, ncol = 2)
```

### AAAS

```{r, ggsci-aaas}
p1_aaas <- p1 + scale_color_aaas()
p2_aaas <- p2 + scale_fill_aaas()
grid.arrange(p1_aaas, p2_aaas, ncol = 2)
```

### NEJM

```{r, ggsci-nejm}
p1_nejm <- p1 + scale_color_nejm()
p2_nejm <- p2 + scale_fill_nejm()
grid.arrange(p1_nejm, p2_nejm, ncol = 2)
```

### Lancet

```{r, ggsci-lancet}
p1_lancet <- p1 + scale_color_lancet()
p2_lancet <- p2 + scale_fill_lancet()
grid.arrange(p1_lancet, p2_lancet, ncol = 2)
```

### JAMA

```{r, ggsci-jama}
p1_jama <- p1 + scale_color_jama()
p2_jama <- p2 + scale_fill_jama()
grid.arrange(p1_jama, p2_jama, ncol = 2)
```

### JCO

```{r, ggsci-jco}
p1_jco <- p1 + scale_color_jco()
p2_jco <- p2 + scale_fill_jco()
grid.arrange(p1_jco, p2_jco, ncol = 2)
```

### UCSCGB

```{r, ggsci-ucscgb}
p1_ucscgb <- p1 + scale_color_ucscgb()
p2_ucscgb <- p2 + scale_fill_ucscgb()
grid.arrange(p1_ucscgb, p2_ucscgb, ncol = 2)
```

### D3

```{r, ggsci-d3}
p1_d3 <- p1 + scale_color_d3()
p2_d3 <- p2 + scale_fill_d3()
grid.arrange(p1_d3, p2_d3, ncol = 2)
```

### LocusZoom

```{r, ggsci-locuszoom}
p1_locuszoom <- p1 + scale_color_locuszoom()
p2_locuszoom <- p2 + scale_fill_locuszoom()
grid.arrange(p1_locuszoom, p2_locuszoom, ncol = 2)
```

### IGV

```{r, ggsci-igv}
p1_igv <- p1 + scale_color_igv()
p2_igv <- p2 + scale_fill_igv()
grid.arrange(p1_igv, p2_igv, ncol = 2)
```

### COSMIC

```{r, ggsci-cosmic}
p1_cosmic_hallmarks_light <- p1 + scale_color_cosmic("hallmarks_light")
p2_cosmic_hallmarks_light <- p2 + scale_fill_cosmic("hallmarks_light")
grid.arrange(p1_cosmic_hallmarks_light, p2_cosmic_hallmarks_light, ncol = 2)

p1_cosmic_hallmarks_dark <- p1 + scale_color_cosmic("hallmarks_dark")
p2_cosmic_hallmarks_dark <- p2 + scale_fill_cosmic("hallmarks_dark")
grid.arrange(p1_cosmic_hallmarks_dark, p2_cosmic_hallmarks_dark, ncol = 2)

p1_cosmic_signature <- p1 + scale_color_cosmic("signature_substitutions")
p2_cosmic_signature <- p2 + scale_fill_cosmic("signature_substitutions")
grid.arrange(p1_cosmic_signature, p2_cosmic_signature, ncol = 2)
```

### UChicago

```{r, ggsci-uchicago}
p1_uchicago <- p1 + scale_color_uchicago()
p2_uchicago <- p2 + scale_fill_uchicago()
grid.arrange(p1_uchicago, p2_uchicago, ncol = 2)
```

### Star Trek

```{r, ggsci-startrek}
p1_startrek <- p1 + scale_color_startrek()
p2_startrek <- p2 + scale_fill_startrek()
grid.arrange(p1_startrek, p2_startrek, ncol = 2)
```

### Tron Legacy

```{r, ggsci-tron}
p1_tron <- p1 +
  theme_dark() +
  theme(
    panel.background = element_rect(fill = "#2D2D2D"),
    legend.key = element_rect(fill = "#2D2D2D"),
    axis.title.x = element_blank(), axis.title.y = element_blank()
  ) +
  scale_color_tron()
p2_tron <- p2 +
  theme_dark() +
  theme(
    panel.background = element_rect(fill = "#2D2D2D"),
    axis.title.x = element_blank(), axis.title.y = element_blank()
  ) +
  scale_fill_tron()

grid.arrange(p1_tron, p2_tron, ncol = 2)
```

### Futurama

```{r, ggsci-futurama}
p1_futurama <- p1 + scale_color_futurama()
p2_futurama <- p2 + scale_fill_futurama()
grid.arrange(p1_futurama, p2_futurama, ncol = 2)
```

### Rick and Morty

```{r, ggsci-rickandmorty}
p1_rickandmorty <- p1 + scale_color_rickandmorty()
p2_rickandmorty <- p2 + scale_fill_rickandmorty()
grid.arrange(p1_rickandmorty, p2_rickandmorty, ncol = 2)
```

### The Simpsons

```{r, ggsci-simpsons}
p1_simpsons <- p1 + scale_color_simpsons()
p2_simpsons <- p2 + scale_fill_simpsons()
grid.arrange(p1_simpsons, p2_simpsons, ncol = 2)
```

### Flat UI

```{r, ggsci-flatui}
p1_flatui <- p1 + scale_color_flatui()
p2_flatui <- p2 + scale_fill_flatui()
grid.arrange(p1_flatui, p2_flatui, ncol = 2)
```

### Frontiers

```{r, ggsci-frontiers}
p1_frontiers <- p1 + scale_color_frontiers()
p2_frontiers <- p2 + scale_fill_frontiers()
grid.arrange(p1_frontiers, p2_frontiers, ncol = 2)
```

### GSEA

```{r}
library("reshape2")

data("mtcars")
cor <- cor(unname(cbind(mtcars, mtcars, mtcars, mtcars)))
cor_melt <- melt(cor)

p3 <- ggplot(cor_melt, aes(x = Var1, y = Var2, fill = value)) +
  geom_tile(colour = "black", linewidth = 0.3) +
  theme_void() +
  theme(axis.title.x = element_blank(), axis.title.y = element_blank())
```

```{r, ggsci-gsea, fig.height=4}
p3_gsea <- p3 + scale_fill_gsea()
p3_gsea_inv <- p3 + scale_fill_gsea(reverse = TRUE)
grid.arrange(p3_gsea, p3_gsea_inv, ncol = 2)
```

### Material Design

```{r, ggsci-material, fig.height=7.12}
set.seed(42)
k <- 9
x <- diag(k)
x[upper.tri(x)] <- runif(sum(1:(k - 1)), 0, 1)
x_melt <- melt(x)

p4 <- ggplot(x_melt, aes(x = Var1, y = Var2, fill = value)) +
  geom_tile(colour = "black", linewidth = 0.3) +
  scale_x_continuous(expand = c(0, 0)) +
  scale_y_continuous(expand = c(0, 0)) +
  theme_bw() +
  theme(
    legend.position = "none", plot.background = element_blank(),
    axis.line = element_blank(), axis.ticks = element_blank(),
    axis.text.x = element_blank(), axis.text.y = element_blank(),
    axis.title.x = element_blank(), axis.title.y = element_blank(),
    panel.background = element_blank(), panel.border = element_blank(),
    panel.grid.major = element_blank(), panel.grid.minor = element_blank()
  )

grid.arrange(
  p4 + scale_fill_material("red"), p4 + scale_fill_material("pink"),
  p4 + scale_fill_material("purple"), p4 + scale_fill_material("deep-purple"),
  p4 + scale_fill_material("indigo"), p4 + scale_fill_material("blue"),
  p4 + scale_fill_material("light-blue"), p4 + scale_fill_material("cyan"),
  p4 + scale_fill_material("teal"), p4 + scale_fill_material("green"),
  p4 + scale_fill_material("light-green"), p4 + scale_fill_material("lime"),
  p4 + scale_fill_material("yellow"), p4 + scale_fill_material("amber"),
  p4 + scale_fill_material("orange"), p4 + scale_fill_material("deep-orange"),
  p4 + scale_fill_material("brown"), p4 + scale_fill_material("grey"),
  p4 + scale_fill_material("blue-grey"),
  ncol = 6
)
```

## Contribute

To contribute to this project, please take a look at the
[Contributing Guidelines](https://nanx.me/ggsci/CONTRIBUTING.html) first.
Please note that the ggsci project is released with a
[Contributor Code of Conduct](https://nanx.me/ggsci/CODE_OF_CONDUCT.html).
By contributing to this project, you agree to abide by its terms.