颜色组柱状图

作者

[编辑] 郑虎;

[审核] .

颜色组柱状图可以用于分组展示数据值，并按顺序标注不同颜色。

环境配置

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

  • 编程语言: R

  • 依赖包: plot3D; ggplotify

# 安装包
if (!requireNamespace("plot3D", quietly = TRUE)) {
  install.packages("plot3D")
}
if (!requireNamespace("ggplotify", quietly = TRUE)) {
  install.packages("ggplotify")
}

# 加载包
library(ggplot2)
library(stringr)

数据准备

数据表格（三列）：

Term | 条目名称，如 GO/KEGG 通路名称

Count | 条目的数值大小，如某通路富集到的基因数

Type | 该通路所属大类：如 BP/MF/CC/KEGG

# 加载数据
data <- read.delim("files/Hiplot/004-barplot-color-group-data.txt", header = T)

# 整理数据格式
colnames(data) <- c("term", "count", "type")
data[,"term"] <- str_to_sentence(str_remove(data[,"term"], pattern = "\\w+:\\d+\\W"))
data[,"term"] <- factor(data[,"term"], 
                        levels =  data[,"term"][length(data[,"term"]):1])
data[,"type"] <- factor(data[,"type"], 
                        levels = data[!duplicated(data[,"type"]), "type"])

# 查看数据
data
                                                  term count type
1                                      Immune response    20   BP
2                        Defense response to bacterium    11   BP
3                                      Cell chemotaxis     8   BP
4                                        Cell adhesion    17   BP
5                                Complement activation     8   BP
6                  Cytokine-mediated signaling pathway     8   MF
7                             Phagocytosis, engulfment     5   MF
8              Negative regulation of jak-stat cascade     5   MF
9                             Epoxygenase p450 pathway     4   MF
10                Chemokine-mediated signaling pathway     6   MF
11  Negative regulation of leukocyte apoptotic process     3   MF
12                   B cell receptor signaling pathway     5   MF
13          Cellular response to tumor necrosis factor     6   CC
14                   Positive regulation of chemotaxis     3   CC
15                 Positive regulation of angiogenesis     6   CC
16                        Collagen fibril organization     4   CC
17 Positive regulation of homotypic cell-cell adhesion    20 KEGG
18              Regulation of cell projection assembly    14 KEGG
19                 Prostate epithelial cord elongation    10 KEGG
20                         Bile acid catabolic process     8 KEGG
21                           Cellular response to drug     7 KEGG
22                 Glycosaminoglycan metabolic process     4 KEGG

可视化

# 三维柱状图
p <- ggplot(data = data, aes(x = term, y = count, fill = type)) +
  geom_bar(stat = "identity", width = 0.8) + 
  theme_bw() +
  xlab("Count") +
  ylab("Term") +
  guides(fill = guide_legend(title="Type")) +
  ggtitle("Barplot Color Group") + 
  coord_flip() +
  theme_classic() +
  scale_fill_manual(values = c("#E64B35FF","#4DBBD5FF","#00A087FF","#3C5488FF")) +
  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,vjust = 1),
        legend.position = "right",
        legend.direction = "vertical",
        legend.title = element_text(size = 10),
        legend.text = element_text(size = 10))

p
图 1: 颜色组柱状图

上图展示了 GO/KEGG 通路富集分析结果的可视化。