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NC图表复现-ggplot2优雅绘制热图(基础入门版)

R语言数据分析指南

2025-06-06

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本节继续来通过NC上的论文介绍常规热图的绘制，数据为论文提供数据，小编根据个人对图形的进行代码编写，结果与原文有所不同，个人观点仅供参考。有需要学习R语言绘图的朋友可关注文末介绍购买小编的R绘图文档。购买前请咨询，零基础不要买。

论文信息

Interspecies hydrogen transfer between cyanobacteria and symbiotic bacteria drives nitrogen lossKong, L., Feng, Y., Zheng, R. et al. Interspecies hydrogen transfer between cyanobacteria and symbiotic bacteria drives nitrogen loss. Nat Commun 16, 5078 (2025). https://doi.org/10.1038/s41467-025-60327-x

原图

仿图

图形解读

此图作为基础版热图，无过多内容可介绍，绘制此图主要在于数据转换如何绘制注释条带，基于此使用分面的形式来进行分组条带的设置，通过将分组文本添加到条带内展示减少图片空间。难度系数一般，属于进阶学习案例。

代码展示

# 加载R包
library(tidyverse)
library(readxl)
library(ggh4x)
library(ggtext)

数据整合

df <- read_excel("41467_2025_60327_MOESM6_ESM.xlsx",sheet ="Fig.6e") %>% 
  select(1:59) %>% 
  pivot_longer(-c(Gene,group2)) %>% 
  mutate(name=str_replace_all(name,"WW","W")) %>% 
  left_join(.,read_tsv("group.tsv") %>% 
              mutate(Sample=str_replace_all(Sample,"WW","W")),
            by=c("name"="Sample"))
# 定义因子
df$name <- factor(df$name,levels = unique(df$name))
df$Gene <- factor(df$Gene,levels = rev(unique(df$Gene)))
df$group <- factor(df$group,levels = unique(df$group))
df$group2 <- factor(df$group2,levels = unique(df$group2))

# 分面条带颜色
strips <- strip_themed(
  background_y = 
    elem_list_rect(fill=c("#EC7A05","#9AC2CD99","#82B7F590","#5A77D190",
                                       "#FAD77B","#16419480")),
  background_x=elem_list_rect(fill=c("#5A77D1","#44007A","#9AC2CD","#6B9B3C",
                                     "#82B7F5")))

热图绘制

ggplot(df,aes(name,Gene,fill=value))+
  geom_tile(color="grey80")+
  facet_grid2(group2~group,scale="free",
              switch="y",strip=strips) +
  force_panelsizes(cols=c(13,13,9,12,10),
                   rows = c(4,6,3,5,5,3),respect=F)+
  scale_x_discrete(expand = c(0,0),
                   position = "top")+
  scale_y_discrete(expand = c(0,0))+
  scale_fill_gradientn(
    colors = c("white", "#e0f3f3", "#66b2a3", "#004c4c", "black"),
    values = scales::rescale(c(0, 0.01, 0.6, 0.95, 1.01)),
    limits = c(0, 1),
    oob = scales::squish,
    breaks = c(0, 0.3, 0.6, 0.9, 1),
    labels = c("0.0", "0.3", "0.6", "0.9", ">1.0")
  )+
  labs(x=NULL,y=NULL) +
  coord_cartesian(clip="off") +
  theme_test() +
  theme(axis.text.x=
          element_text(color="black",angle = 45,
                       vjust=0.5,hjust =0,size=7),
        axis.text.y=element_text(color="black",size=7),
        strip.placement = "outside",
        axis.ticks = element_blank(),
        panel.spacing.x = unit(0,"cm"),
        panel.spacing.y = unit(0,"cm"),
        strip.text.x = 
          element_text(color="white",size=10,face="bold"),
        strip.text.y = element_markdown(color="black",size=7),
        strip.background = element_rect(color="white"),
        legend.background = element_blank(),
        legend.title = element_blank(),
        legend.key.height = unit(1,"null"))