渐变柱状图

作者

[编辑] 郑虎;

[审核] .

同气泡图相似，不过是在柱状图的基础上，用颜色渐变的长方形同时展示两个变量的可视化图形。

环境配置

  • 系统: Cross-platform (Linux/MacOS/Windows)

  • 编程语言: R

  • 依赖包: ggplot2; stringr

# 安装包
if (!requireNamespace("ggplot2", quietly = TRUE)) {
  install.packages("ggplot2")
}
if (!requireNamespace("stringr", quietly = TRUE)) {
  install.packages("stringr")
}

# 加载包
library(ggplot2)
library(stringr)

数据准备

案例数据，第一列为Go Term（Go语言编号），第二列为基因数，第三列输入pvalue。

# 加载数据
data <- read.delim("files/Hiplot/008-barplot-gradient-data.txt", header = T)

# 整理数据格式
data[, 1] <- str_to_sentence(str_remove(data[, 1], pattern = "\\w+:\\d+\\W"))
topnum <- 7
data <- data[1:topnum, ]
data[, 1] <- factor(data[, 1], level = rev(unique(data[, 1])))

# 查看数据
head(data)
                               Term Count   PValue
1                   Immune response    20 9.61e-08
2     Defense response to bacterium    11 3.02e-06
3                   Cell chemotaxis     8 5.14e-06
4                     Cell adhesion    17 2.73e-05
5             Complement activation     8 3.56e-05
6 Extracellular matrix organization    11 4.23e-05

可视化

# 渐变柱状图
p <- ggplot(data, aes(x = Term, y = Count, fill = -log10(PValue))) +
  geom_bar(stat = "identity") +
  ggtitle("GO BarPlot") +
  scale_fill_continuous(low = "#00438E", high = "#E43535") +
  scale_x_discrete(labels = function(x) {str_wrap(x, width = 65)}) +
  labs(fill = "-log10 (PValue)", y = "Term", x = "Count") +
  coord_flip() +
  theme_bw() +
  theme(text = element_text(family = "Arial"),
        plot.title = element_text(size = 12,hjust = 0.5),
        axis.title = element_text(size = 12),
        axis.text = element_text(size = 10),
        axis.text.x = element_text(angle = 0, hjust = 0.5),
        legend.position = "right",
        legend.direction = "vertical",
        legend.title = element_text(size = 10),
        legend.text = element_text(size = 10))

p
图 1: 渐变柱状图

如图示，蓝色为低pvalue颜色，红色为高pvalue颜色，随着pvalue增大颜色由蓝向红渐变。横坐标表示基因数目。