如何试用 R 语言绘制散点图

#读取示例数据

express <- read.delim('gene_diff.txt', sep = '	')

#将基因表达值取个log(1+)转换

express$control <- log(express$control+1)

express$treat <- log(express$treat+1)

#排序，目的是将显著的基因展示在前方图层，避免被不显著基因的点遮盖

express$diff <- factor(express$diff, levels = c('up', 'down', 'none'))

express <- express[order(express$diff, decreasing = TRUE), ]

head(express)  #查看读取并预处理后的数据表格

#绘制散点图，显著上、下调基因以不同颜色区分

library(ggplot2)

ggplot(express, aes(x = control, y = treat)) +

geom_point(aes(color = diff), size = 1) +  #按上下调指定基因点的颜色

scale_color_manual(values = c('red', 'gray', 'green4'), limit = c('up', 'none', 'down')) +  #上下调基因颜色赋值

theme_bw() +  #背景调整

labs(x = 'control group', y = 'treat group', color = '') +  #坐标轴标题设置

geom_abline(intercept = 1, slope = 1, col = 'black', linetype = 'dashed', size = 0.5) +  #这3句用于添加 |log2FC|>1 的阈值线

geom_abline(intercept = -1, slope = 1, col = 'black', linetype = 'dashed', size = 0.5) +

geom_abline(intercept = 0, slope = 1, col = 'black', linetype = 'dashed', size = 0.5)

#按 p 值数值的渐变色散点图

ggplot(express, aes(x = control, y = treat)) +

geom_point(aes(color = pvalue), size = 0.8) +  #按 p 值大小指定基因点的颜色

scale_color_gradient2(low = 'red', mid = 'darkgoldenrod2', high = 'royalblue2', midpoint = 0.5) +  #渐变色颜色指定

theme_bw() +  #背景调整

labs(x = 'control group', y = 'treat group', color = 'p-value') +  #坐标轴标题设置

geom_abline(intercept = 1, slope = 1, col = 'black', linetype = 'dashed', size = 0.5) +  #这3句用于添加 |log2FC|>1 的阈值线

geom_abline(intercept = -1, slope = 1, col = 'black', linetype = 'dashed', size = 0.5) +

geom_abline(intercept = 0, slope = 1, col = 'black', linetype = 'dashed', size = 0.5)