之前有小伙伴咨询了一个韦恩图，其实韦恩图很简单，很多在线工具，代码的话不论是R还是python都有各种各样的包或者方法实现作图。但是他的需求是如何指示文字，一般的方法当然是使用AI很方便，但是代码可不可以实现呢？答案是肯定的！这里我们介绍一下使用ggveen/ggplot实现韦恩图的做法，并添加指示文字！参考：
https://www.bilibili.com/video/BV1TC4y1N7b2/?spm_id_from=333.999.0.0&vd_source=05b5479545ba945a8f5d7b2e7160ea34
首先我们构建一个差异基因分析，用来做韦恩图：
celltype_DEGs <- list()
cells <- c("UEC", "CEC")
for (i in 1:2) {
data = subset(sce, celltype==cells[i])
df <- FindMarkers(data,
group.by="orig.ident",
ident.1="AEH",
ident.2="HC",
logfc.threshold = 0.4,
min.pct = 0.4)
celltype_DEGs[[i]] <- df
}
# adjust p 显著
for(i in seq_along(celltype_DEGs)){
celltype_DEGs[[i]] <- celltype_DEGs[[i]][which(celltype_DEGs[[i]]$p_val_adj<=0.05),]
}
我们直接使用ggvenn作图：
library(ggvenn)
library(tidyverse)
library(ggtext)
Venn_list <- list(UEC=rownames(celltype_DEGs[[1]]),
CEC=rownames(celltype_DEGs[[2]]))
#使用list_to_data_frame将list转化为data.frame
data_veen = list_to_data_frame(Venn_list)
#鉴定集合基因
Common_gene <- data_veen[which(data_veen$`UEC`=="TRUE" & data_veen$`CEC`=="TRUE"),]
UEC_gene <- data_veen[which(data_veen$`UEC`=="TRUE" & data_veen$`CEC`=="FALSE"),]
CEC_gene <- data_veen[which(data_veen$`UEC`=="FALSE" & data_veen$`CEC`=="TRUE"),]
#保存文件
write.csv(Common_gene, file = "Common_gene.csv")
write.csv(UEC_gene, file = "UEC_gene.csv")
write.csv(CEC_gene, file = "CEC_gene.csv")
#method1,用list数据、ggvenn作图
ggvenn(Venn_list,
show_percentage = T,
show_elements = F,
text_size=3,
digits = 1,
auto_scale =T,
set_name_size=4,
stroke_color = "grey30",
fill_color = c("#FF8C00","#4DAF4A"),
set_name_color = c("#FF8C00","#4DAF4A"))+
geom_segment(aes(x = 0.2, y = -0.2,xend = 0.2,yend = -0.8),
arrow = arrow(length = unit(0.07, "inch")),size = 1,
color = "grey30")+
geom_text(aes(0.2, -1, label = "ASTL GCLC\nIGFBP4 PDE4C\nMMP7 TRH"),
hjust = -0.2, vjust =0, fontface="italic")+
geom_curve(aes(x = -1, y = 0,xend = -0.5,yend = 1.8),
arrow = arrow(length = unit(0.1, "inch")),size = 1,
color = "grey30", curvature = -0.4)+
geom_text(aes(-0.5, 2, label = "SYT14 MUC16\nPCDH7 HPN\nITGA6 CXCL3"),
hjust = -0.1, vjust =1, fontface="italic")+
geom_curve(aes(x = 1, y = 0,xend = 0.5,yend = 1),
arrow = arrow(length = unit(0.1, "inch")),size = 1,
color = "grey30", curvature = 0.2)+
geom_text(aes(0.5, 1, label = "CASC9 SFTA2\nCOL1A1 SPARC"),
hjust = 1, vjust =-0.1, fontface="italic")
使用ggplot，geom_veen作图：
p = ggplot(data_veen, aes(A = `UEC`, B = `CEC`)) +
geom_venn(auto_scale =T,
set_name_size=4,
fill_color = c("#BCCC35","#5DBBA1"),
set_name_color = c("#BCCC35","#5DBBA1")) +
theme_void() +
coord_fixed()+
geom_segment(aes(x = 0.2, y = -0.2,xend = 0.2,yend = -1),
arrow = arrow(length = unit(0.07, "inch")),size = 1,
color = "grey30")+
geom_text(aes(0.2, -1.2, label = "ASTL GCLC\nIGFBP4 PDE4C\nMMP7 TRH"),
hjust = 0.5, vjust =1, fontface="italic")+
geom_curve(aes(x = -1, y = 0,xend = -0.5,yend = 1.8),
arrow = arrow(length = unit(0.1, "inch")),size = 1,
color = "grey30", curvature = -0.4)+
geom_text(aes(-0.5, 2, label = "SYT14 MUC16\nPCDH7 HPN\nITGA6 CXCL3"),
hjust = -0.1, vjust =1, fontface="italic", color="#BCCC35")+
geom_curve(aes(x = 1, y = 0,xend = 1.2,yend = 1),
arrow = arrow(length = unit(0.1, "inch")),size = 1,
color = "grey30", curvature = 0.2)+
geom_text(aes(1.2, 1, label = "CASC9 SFTA2\nCOL1A1 SPARC"),
hjust = -0.1, vjust =1, fontface="italic", color="#5DBBA1")
最后，我们还以添加矢量图表示不同的样本：简笔画网站：
http://phylopic.org/image/browse/
#读入图片
library(grid)
library(png)
library(RCurl)
rayur1 = "https://images.phylopic.org/images/9fae30cd-fb59-4a81-a39c-e1826a35f612/raster/187x512.png"
raylogo1 = readPNG(getURLContent(rayur1), native = T)
im1 <- rasterGrob(raylogo1, interpolate=TRUE)
rayur2 = "https://images.phylopic.org/images/acf1cbec-f6ef-4a82-8ab5-be2f963b93f5/raster/192x512.png"
raylogo2 = readPNG(getURLContent(rayur2), native = T)
im2 <- rasterGrob(raylogo2, interpolate=TRUE)
p+
annotation_custom(im1, xmin=-1.8, xmax=-1.3, ymin=-0.5, ymax=0.5)+
annotation_custom(im2, xmin=1.1, xmax=1.6, ymin=-0.5, ymax=0.5)
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