R语言ggplot2优雅的绘制高端气泡图

数据和代码获取：请查看主页个人信息！！！

大家好，今天我将介绍如何使用R语言ggplot2包绘制精美的文本表+气泡组合图。

大家在分析绘图的时候是否看到过类似这样的图片，该图在气泡图的基础上增加了文本信息，属于“表格+图片”组合体，

展示了很多信息：

图片来源：Microbial community analysis of anaerobic reactors treating soft drink wastewater

今天我们使用微生物组数据进行模仿展示，接下来我们来进行分析和可视化展示：

Step1：数据载入

rm(list = ls())pacman::p_load(tidyverse,reshape2,cowplot,aplot)otu <- read.csv("OTU.csv")sample_info <- read.csv("sample_info.csv",row.names = 1)tax <- read.csv("tax.csv")

Step2：数据准备

df1 <-   otu %>%  column_to_rownames(var = "ID") %>%  mutate(sum = rowSums(.)) %>%  select(sum) %>%   arrange(desc(sum)) %>%   top_n(20)
df2 <-   tax %>%   filter(ID %in% rownames(df1))

Step3：绘制气泡图

p1 <-  otu %>%  left_join(df2) %>%   mutate(ID = factor(ID, levels = ID,  ordered = T)) %>%  filter(ID %in% rownames(df1)) %>%   reshape2::melt() %>%   filter(value != 0) %>%  ggplot() +   geom_point(aes(x = variable, y = ID, fill = ID, size = value), shape = 21) +   scale_size_area(max_size = 5) +  scale_x_discrete(position = "top") +  geom_point(aes(x = variable, y = ID,fill = ID, size = value), shape = 21) +   labs(x = "", y = "") +   guides(fill = "none",         size = guide_legend(ncol = 1)) +   theme_bw() +   theme(panel.grid = element_blank(),        axis.text.x.top = element_text(size = 6, angle = 45, hjust = 0, color = "black"),        axis.text.y.right = element_text(size = 10, color = "black"),        axis.ticks = element_blank(),        axis.text.y = element_blank())

Step4：绘制OTU汇总信息

# 绘制OTU信息p2 <-   df1 %>%   mutate(ID = factor(rownames(.), levels = rownames(.),  ordered = T)) %>%  ggplot() +   geom_text(aes(x = "Size", y = ID, label = sum), size = 3) +   scale_x_discrete(position = "top") +  labs(x = "", y = "") +   annotate(geom = "rect", xmin = 0.5, xmax = 1.5, ymin = 0.5, ymax = Inf, fill = "grey", alpha = 0.2) +  theme_nothing() +   theme(panel.grid = element_blank(),        axis.text.x.top = element_text(size = 10),        axis.ticks = element_blank())
p_size <-   p2 +  geom_hline(yintercept = c(21.5, 20.5, 0.5), size = 1) +  geom_hline(yintercept = c(19.5, 18.5, 15.5, 13.5, 12.5, 11.5, 9.5, 8.5, 7.5, 4.5, 2.5), size = 0.5, linetype = 'dashed', color = 'black')
p3 <-   df2 %>%   ggplot() +   geom_text(aes(x = 'OTU', y = ID, label = ID), size = 3) +  scale_x_discrete(position = "top") +  labs(x = "", y = "") +   theme_nothing() +   theme(panel.grid = element_blank(),        axis.text.x.top = element_text(size = 10),        axis.ticks = element_blank())
p_OTU <-   p3 +  geom_hline(yintercept = c(22.5, 21.5, 20.5, 0.5), size = 1) +  geom_hline(yintercept = c(19.5, 18.5, 15.5, 13.5, 12.5, 11.5, 9.5, 8.5, 7.5, 4.5, 2.5), size = 0.5, linetype = 'dashed', color = 'black')
p_size %>%   insert_right(p_OTU)ggsave('pic2.png', width = 2, height = 3.5, bg = 'white')

Step5：绘制OTU分类信息

pic <- function(level){  df2 %>%     select(c(level, 'ID')) %>%     set_names(c('label', 'ID')) %>%     mutate(Info = str_split(label, pattern = "_", simplify = T)[,3]) %>%    ggplot() +     geom_text(aes(x = level, y = ID, label = Info), size = 3) +    scale_x_discrete(position = "top") +    labs(x = "", y = "") +     theme_nothing() +     theme(panel.grid = element_blank(),          axis.text.x.top = element_text(size = 10),          axis.ticks = element_blank())}
p_Class <-   pic('Class') +  geom_hline(yintercept = c(21.5, 20.5, 0.5), size = 1) +  geom_hline(yintercept = c(19.5, 18.5, 15.5, 13.5, 12.5, 11.5, 9.5, 8.5, 7.5, 4.5, 2.5), size = 0.5, linetype = 'dashed', color = 'black')
p_Order <-   pic('Order') +  geom_hline(yintercept = c(21.5, 20.5, 0.5), size = 1) +  geom_hline(yintercept = c(19.5, 18.5, 15.5, 13.5, 12.5, 11.5, 9.5, 8.5, 7.5, 4.5, 2.5), size = 0.5, linetype = 'dashed', color = 'black')
p_Family <-   pic('Family') +  geom_hline(yintercept = c(21.5, 20.5, 0.5), size = 1) +  geom_hline(yintercept = c(19.5, 18.5, 15.5, 13.5, 12.5, 11.5, 9.5, 8.5, 7.5, 4.5, 2.5), size = 0.5, linetype = 'dashed', color = 'black')
p_Class %>%   insert_right(p_Order) %>%   insert_right(p_Family)ggsave('pic3.png', width = 6, height = 3.5, bg = 'white')

因为微生物Class/Order/Family数据结构一样，因此我们定义了一个pic()函数，达到简化代码的目的，可视化效果如下：

Step6：组合

p_Class %>%   insert_right(p_Order) %>%   insert_right(p_Family) %>%   insert_right(p_OTU, width = 0.3) %>%   insert_right(p_size, width = 0.3) %>%   insert_right(p1, width = 6)ggsave(filename = "plot.png", height = 6, width = 15)

由于样品数量较多，所以效果比较差，接下来我们尝试按照样本分组求和绘图：

Step7：组合（分组）

p_type <-    otu %>%   filter(ID %in% rownames(df1)) %>%   column_to_rownames('ID') %>%   t() %>%   as.data.frame() %>%   rownames_to_column('SampleID') %>%   left_join(sample_info) %>%   group_by(Type) %>%   summarise_if(is.numeric, sum, na.rm = TRUE) %>%   reshape2::melt() %>%   ggplot() +   geom_point(aes(x = Type, y = variable,fill = Type, size = value), shape = 21) +   scale_size_area(max_size = 10) +  annotate(geom = "rect", xmin = 0.5, xmax = 1.5, ymin = 0.5, ymax = Inf, fill = "grey", alpha = 0.2) +  annotate(geom = "rect", xmin = 2.5, xmax = 3.5, ymin = 0.5, ymax = Inf, fill = "grey", alpha = 0.2) +  annotate(geom = "rect", xmin = 4.5, xmax = 5.5, ymin = 0.5, ymax = Inf, fill = "grey", alpha = 0.2) +  scale_x_discrete(position = "top") +  ggsci::scale_fill_nejm() +  labs(x = "", y = "") +   guides(fill = "none",         size = guide_legend(ncol = 1)) +   theme_bw() +   theme(panel.grid = element_blank(),        axis.text.x.top = element_text(size = 10, angle = 45, hjust = 0, color = "black"),        axis.text.y.right = element_text(size = 10, color = "black"),        axis.ticks = element_blank(),        axis.text.y = element_blank())p_type
p_Class %>%   insert_right(p_Order) %>%   insert_right(p_Family) %>%   insert_right(p_OTU, width = 0.3) %>%   insert_right(p_size, width = 0.3) %>%   insert_right(p_type, width = 2)ggsave(filename = "plot_by_type.png", height = 6, width = 10)

现在整体效果看上去舒服多了~

数据和代码获取：请查看主页个人信息！！！

关键词“气泡图”获得本期代码和数据。