目录

使用linkET绘制相关性+mantel检验组合图

简介

本页直接使用了老师提供的相关性矩阵和mantel检验的结果。 heatmap.txt network.txt

如果没有这两个文件，可参考https://github.com/Hy4m/linkET 

数据样式可参考
library(vegan)
data("varechem", package = "vegan")
data("varespec", package = "vegan")

linkET下载安装

install.packages("devtools")
library(devtools)
devtools::install_github("Hy4m/linkET", force = TRUE)
packageVersion("linkET")

绘图

setwd("/Users/l_l_/Desktop")
dh<-read.table("heatmap.txt",header = T,row.names = 1)
dn<-read.table("network.txt",header = T,sep='\t')
 
library(ggplot2)
library(linkET)
 
#热图部分
p <- qcorrplot(as.matrix(dh), 
               type = "upper",      
               diag = FALSE,
               grid_size = 0.25)+   
  geom_square() +
#网络部分
  geom_couple(aes(colour = pd, size = rd), 
              data = dn, 
              curvature = nice_curvature(),   
              label.size = 3)+       
  scale_fill_gradientn(colours = RColorBrewer::brewer.pal(11, "RdBu")) +
  scale_size_manual(values = c(0.5, 1, 2)) +   
  scale_colour_manual(values = color_pal(3)) +
#图例
  guides(size = guide_legend(title = "Mantel's r",
                             override.aes = list(colour = "grey35"), 
                             order = 2),
         colour = guide_legend(title = "Mantel's p", 
                               override.aes = list(size = 3), 
                               order = 1),
         fill = guide_colorbar(title = "Pearson's r", order = 3))
 
ggsave("linKET.png",p,dpi = 1000)
ggsave('linkET.pdf',p,dpi = 1000)

结果

linket.pdf