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

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)")