R包：ggsci期刊配色

介绍

不同期刊配色大多数时候不一样，为了更好符合期刊图片颜色的配色，有人开发了ggsci这个R包。它提供以下函数：

• scale_color_palname()

• scale_fill_palname()

对应不同期刊的color和fill函数。

导入数据+R包

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, size = 1, span = 1) +
      theme_bw()

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()

NPG: Nature Publishing Group

p1_npg <- p1 + scale_color_npg()
p2_npg <- p2 + scale_fill_npg()
grid.arrange(p1_npg, p2_npg, ncol = 2)

AAAS: American Association for the Advancement of Science

p1_aaas <- p1 + scale_color_aaas()
p2_aaas <- p2 + scale_fill_aaas()
grid.arrange(p1_aaas, p2_aaas, ncol = 2)

NEJM:The New England Journal of Medicine

p1_nejm <- p1 + scale_color_nejm()
p2_nejm <- p2 + scale_fill_nejm()
grid.arrange(p1_nejm, p2_nejm, ncol = 2)

Lancet: Lancet journals

p1_lancet <- p1 + scale_color_lancet()
p2_lancet <- p2 + scale_fill_lancet()
grid.arrange(p1_lancet, p2_lancet, ncol = 2)

JAMA: The Journal of the American Medical Association

p1_jama <- p1 + scale_color_jama()
p2_jama <- p2 + scale_fill_jama()
grid.arrange(p1_jama, p2_jama, ncol = 2)

UCSCGB: UCSC Genome Browser

p1_ucscgb <- p1 + scale_color_ucscgb()
p2_ucscgb <- p2 + scale_fill_ucscgb()
grid.arrange(p1_ucscgb, p2_ucscgb, ncol = 2)

Tron Legacy

p1_tron <- p1 + theme_dark() + theme(
    panel.background = element_rect(fill = "#2D2D2D"),
    legend.key = element_rect(fill = "#2D2D2D")) +
  scale_color_tron()
p2_tron <- p2 + theme_dark() + theme(
    panel.background = element_rect(fill = "#2D2D2D")) +
  scale_fill_tron()
grid.arrange(p1_tron, p2_tron, ncol = 2)

GSEA: GSEA GenePattern

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", size = 0.3) +
  theme_bw() +
  theme(axis.title.x = element_blank(),
        axis.title.y = element_blank())

p3_gsea <- p3 + scale_fill_gsea()
p3_gsea_inv <- p3 + scale_fill_gsea(reverse = TRUE)
grid.arrange(p3_gsea, p3_gsea_inv, ncol = 2)

Reference

1. ggsci