R语言绘图

多组火山图

数据准备:

将CSV文件同一在一个路径下,用代码合并

确保文件列名正确

R 复制代码
library(fs)
library(dplyr)
library(tidyr)
library(stringr)
library(ggplot2)
library(ggfun)
library(ggrepel)

# 获取文件列表
file_paths <- dir_ls(path = "E:\\proteomic\\fuxian_bacteria\\multivolcano", pattern = "_DEG\\.csv$", full.names = T)
# 检查文件列表
print(file_paths)

# 读取和处理数据
all_deg <- map(file_paths, function(x){
  # 检查文件扩展名,忽略大小写
  if (str_ends(str_to_lower(x), ".csv")) {
    cat("Processing file:", x, "\n") # 打印正在处理的文件名
    data <- read_delim(file = x, col_names = T, delim = ",")
    if (is.data.frame(data)) {
      group <- str_remove(basename(x), pattern = "_DEG.*")
      return(dplyr::mutate(data, group = group))
    } else {
      cat("Failed to read file:", x, "\n")
      return(NULL)
    }
  } else {
    cat("Skipping non-CSV file:", x, "\n")
    return(NULL)
  }
}) %>%
  compact() %>% # 移除列表中的 NULL 元素
  do.call(rbind, .)

ggplot(data = all_deg) +
  geom_jitter(data = all_deg %>% dplyr::filter(change == "Normal"),
              aes(x = group, y = logFC, color = change, size = abs(logFC), alpha = abs(logFC)),
              width = 0.4) +
  geom_jitter(data = all_deg %>% dplyr::filter(change != "Normal"),
              aes(x = group, y = logFC, color = change, size = abs(logFC), alpha = abs(logFC)),
              width = 0.4) +
  geom_jitter(data = all_deg %>% dplyr::group_by(group) %>%
                dplyr::arrange(desc(abs(logFC))) %>%
                dplyr::slice_head(n = 15) %>%
                dplyr::ungroup() %>%
                na.omit(),
              aes(x = group, y = logFC, size = abs(logFC)),
              width = 0.4, shape = 21, fill = "#e77381") +
  geom_text_repel(data = all_deg %>% dplyr::group_by(group) %>%
                    dplyr::arrange(desc(abs(logFC))) %>%
                    dplyr::slice_head(n = 15) %>%
                    dplyr::ungroup() %>%
                    na.omit(),
                  aes(x = group, y = logFC, label = SYMBOL)) +
  geom_tile(aes(x = group, y = 0, fill = group), height = 0.4) +
  geom_text(data = all_deg %>% dplyr::select(group) %>% dplyr::distinct(group, .keep_all = T),
            aes(x = group, y = 0, label = group), size = 6) +
  geom_hline(yintercept = c(-log2(1.5), log2(1.5))) +
  scale_y_continuous(limits = c(-5, 5)) +
  scale_size(range = c(1, 10)) +
  scale_alpha(range = c(0.1, 1)) +
  scale_color_manual(values = c("Up" = "#f46d43", "Normal" = "#bdbdbd", "Down" = "#3288bd")) +
  scale_fill_manual(values = c('#8dd3c7','#ffffb3','#bebada','#fb8072','#80b1d3')) +
  theme_bw() +
  theme(axis.text = element_text(color = "#000000", size = 12),
        axis.title = element_text(color = "#000000", size = 15),
        panel.grid = element_blank(),
        legend.background = element_roundrect(color = "#969696")) +
  labs(y = "log2(Fold Change)")
相关推荐
Shartin1 分钟前
CPT208-Human-Centric Computing: Prototype Design Optimization原型设计优化
开发语言·javascript·原型模式
dme.13 分钟前
Javascript之DOM操作
开发语言·javascript·爬虫·python·ecmascript
teeeeeeemo18 分钟前
回调函数 vs Promise vs async/await区别
开发语言·前端·javascript·笔记
加油吧zkf23 分钟前
AI大模型如何重塑软件开发流程?——结合目标检测的深度实践与代码示例
开发语言·图像处理·人工智能·python·yolo
ejinxian38 分钟前
PHP 超文本预处理器 发布 8.5 版本
开发语言·php
软件黑马王子1 小时前
C#系统学习第八章——字符串
开发语言·学习·c#
阿蒙Amon1 小时前
C#读写文件:多种方式详解
开发语言·数据库·c#
Da_秀1 小时前
软件工程中耦合度
开发语言·后端·架构·软件工程
Fireworkitte1 小时前
Java 中导出包含多个 Sheet 的 Excel 文件
java·开发语言·excel
运器1233 小时前
【一起来学AI大模型】算法核心:数组/哈希表/树/排序/动态规划(LeetCode精练)
开发语言·人工智能·python·算法·ai·散列表·ai编程