代码语言：javascript复制❝本节来介绍如何绘图韦恩点图及对其进行注释，图表主要使用「ggplot2」,「UpSetR」，「ggplotify」等包来实现，
此图我想介绍的重点在于图形格式的转换及拼图下面来进行具体介绍， A highly conserved core bacterial microbiota with nitrogen-fixation capacity inhabits the xylem sap in maize plants ❞
library(tidyverse)
library(UpSetR)
library(ggplotify)
library(cowplot)
library(ggrepel)
otu_RA <- read_tsv("data.xls") %>% column_to_rownames(var="OTUID")
绘制韦恩点图
代码语言：javascript复制p1 <- UpSetR::upset(otu_RA,
nset = 7, # 集合数
nintersects = 10, # 绘制交叉数目
order.by = "freq", # 排序方式
mb.ratio = c(0.7,0.3), # 条形图与点图之间的比例
point.size = 1.8,line.size = 1,mainbar.y.label = "Intersection size",
sets.x.label = "Set Size",
main.bar.color = "#2a83a2",
sets.bar.color = "#3b7960",
queries = list(list(query = intersects,
params = list("BS","RS","RE","VE","SE","LE","P"),
active = T,color="#d66a35",
query.name = "BS vs RS vs RE vs VE vs SE vs LE vs P")))
绘制圈图
代码语言：javascript复制p2 <- tribble(~group, ~perc,~A,
"24%",24,5,
"76%",76,5) %>%
ggplot(aes(A,perc,fill=group))
geom_col()
coord_polar(theta="y")
xlim(0,6)
labs(title="Number of overlapped OTUs:1364nNumber of total OTUs in xylem: 1792")
scale_fill_manual(values=c("#75C500","#5686C3"))
theme_void()
theme(legend.position = "non",
plot.title = element_text(hjust=0.5,vjust=-62,color="black",size=6.8),
plot.margin = unit(c(-2,0,-1,0),unit="cm"))
geom_text_repel(data=. %>% filter(group=="76%"),
aes(label=group,x=5,y=60),
nudge_x=-2.5,
nudge_y=0,size=4,
box.padding = 1,segment.curvature=-0.1,hjust=1)
拼图
代码语言：javascript复制p1 %>% as.grob() %>% ggdraw()
theme(plot.margin = unit(c(0,0,-0.8,-3),unit="cm"))
draw_plot(p2,scale=0.4,x=0.25,y=0.22)
图像导出
代码语言：javascript复制ggsave(file="venn.pdf",width=5.6,height=4.3,unit="in",dpi=300)
数据导出
代码语言：javascript复制otu_select <- read_tsv("data.xls") %>% filter_all(all_vars(. > 0))
write.table(as.matrix(otu_select),"otu_overlap.txt",sep = 't',quote = FALSE,col.names = NA)
❝好了本节介绍到此结束，当然还是存在一点小bug这个以后在想办法解决了
