论文原文
图形解读
❝作为常见的相关性热图，此图在细节方面做了调整，用星代替以往的点来表示R值，同时通过透明度来调节梯度，线条也根据P值大小做了调节。 ❞
加载R包
代码语言：javascript复制library(tidyverse)
library(linkET)
library(psych)
library(reshape2)
library(magrittr)
library(ggtext)
library(ggstar)
library(ggnewscale)
导入数据
代码语言：javascript复制env <- read_tsv("env.tsv")
spe <- read_tsv("spe.tsv")
数据清洗
代码语言：javascript复制pp <- corr.test(spe,env,method="pearson",adjust = "fdr")
cor <- pp$r
pvalue <- pp$p
df <- melt(cor) %>% mutate(pvalue=melt(pvalue)[,3],
p_signif=symnum(pvalue, corr = FALSE, na = FALSE,
cutpoints = c(0, 0.001, 0.01, 0.05, 0.1, 1),
symbols = c("***", "**", "*", "", " "))) %>%
set_colnames(c("env","genus","r","p","p_signif"))
cordata <- df %>%
filter(genus %in% c("N","K","Ca")) %>%
select(2,1,3,4,5) %>%
mutate(rd = cut(r, breaks = c(-Inf, 0, 0.4, Inf),
labels = c("< 0", "0 - 0.4", ">= 0.4")),
pd = cut(p, breaks = c(-Inf, 0.05, Inf),
labels = c("< 0.05",">= 0.05")))
数据可视化
代码语言：javascript复制qcorrplot(correlate(spe,method = "pearson"),diag=F,type="lower")
geom_star(aes(size=r,fill=r,alpha=r),color=NA)
scale_fill_gradientn(colours = rev(RColorBrewer::brewer.pal(11,"RdBu")))
new_scale_fill()
geom_couple(aes(colour=pd,linetype=pd),data=cordata,label.colour = "black",
curvature=nice_curvature(0.1),nudge_x=0.3,
label.fontface=2,
label.size =3,drop =T)
scale_colour_manual(values =c("red","#1B9E77"))
scale_linetype_manual(values = c("solid","dashed"))
guides(size = guide_legend(title = " ",override.aes = list(colour = "grey35"), order = 2),
colour = guide_legend(title = "Mantel's p",override.aes = list(size = 3), order = 1),
linetype=guide_legend(title = "Mantel's p",override.aes = list(size = 3), order = 1),
alpha = "none")
theme(plot.margin = unit(c(0,-3,0,-2),units="cm"),
panel.background = element_blank(),
plot.background = element_blank(),
axis.text=element_markdown(color="black",size=8,face="bold"),
legend.background = element_blank(),
legend.key = element_blank(),
legend.title = element_text(margin = margin(b= 5)),
legend.spacing.y = unit(0,"cm"),
legend.key.height = unit(0.5,"cm"))
