矩阵气泡图

作者

[编辑] 郑虎;

[审核] .

注记

Hiplot 网站

本页面为 Hiplot Matrix Bubble 插件的源码版本教程，您也可以使用 Hiplot 网站实现无代码绘图，更多信息请查看以下链接:

https://hiplot.cn/basic/matrix-bubble?lang=zh_cn

彩色矩阵气泡用于可视化不同细胞（列）中多个基因（行）的表达矩阵数据。

环境配置

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

  • 编程语言: R

  • 依赖包: ggalluvial; ggplot2

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

# 加载包
library(ggalluvial)
library(ggplot2)

数据准备

数据结构：

  • <1st-col>: (String) 单元格样本名称作为 X 轴
  • <2nd-col>: (String) 基因名作为Y轴
  • <3rd-col>: (Numeric) 基因表达
  • <4rd-col>: (Numeric) 组
# 加载数据
data <- read.delim("files/Hiplot/118-matrix-bubble-data.txt", header = T)

# 整理数据格式
data[, 1] <- factor(data[, 1], levels = unique(data[, 1]))
data[, 2] <- factor(data[, 2], levels = unique(data[, 2]))

# 查看数据
head(data)
      x     y value  group
1 cell1 gene1     1 groupC
2 cell1 gene2     5 groupC
3 cell1 gene3    10 groupC
4 cell1 gene4    15 groupC
5 cell1 gene5    20 groupC
6 cell1 gene6    25 groupC

可视化

# 矩阵气泡图
p <- ggplot(data = data, aes(x = x, y = y, size = value, color = y)) +
  geom_point(alpha = 1) +
  labs(title = "Matrix Bubble") +
  guides(color = FALSE) +
  theme(panel.background = element_blank(),
        panel.grid.major = element_line(colour = "gray"),
        strip.background = element_blank(),
        panel.border = element_rect(colour = "black", fill = NA),
        panel.spacing = unit(0, "lines"),
        plot.title = element_text(size = 12, hjust = 0.5),
        text = element_text(family = "Arial"),
        legend.title = element_text(size = 10),
        axis.text.x = element_text(angle=0, hjust=0.5, vjust=1)) +
  facet_grid(~group, scales = 'fixed', margins = F) +
  scale_color_manual(values = c(
    "#3B4992FF","#EE0000FF","#008B45FF","#631879FF","#008280FF","#BB0021FF",
    "#5F559BFF","#A20056FF","#808180FF","#1B1919FF"))

p
图 1: 矩阵气泡图