论文
Changes in plant inputs alter soil carbon and microbial communities in forest
本地pdf Global Change Biology - 2022 - Feng - Changes in plant inputs alter soil carbon and microbial communities in forest.pdf
今天的推文重复一下论文中的Figure3，这个是之前有读者在公众号后台的留言，之前我不知道怎么实现这种好几个子图中间没有空白的形式，有读者留言可以用分面然后调节主题里的参数panel.spacing = unit(0,'lines')，有了基本思路就可以尝试一下这个图
image.png
今天的推文主要介绍如何给每个分面单独添加注释，这里需要用到一个自定义函数
annotation_custom2 <- function (grob,
xmin = -Inf,
xmax = Inf,
ymin = -Inf,
ymax = Inf,
data)
{
layer(data = data,
stat = StatIdentity,
position = PositionIdentity,
geom = ggplot2:::GeomCustomAnn,
inherit.aes = TRUE, params = list(grob = grob,
xmin = xmin, xmax = xmax,
ymin = ymin, ymax = ymax))
}
之前的推文的代码
library(readxl)
dat<-read_excel("data/20220804/example_df.xlsx")
dat
library(ggplot2)
ggplot(data=dat,aes(x=x,y=y))+
geom_errorbarh(aes(xmin=x-sd_value,
xmax=x+sd_value,
color=group02),
height=0,
show.legend = FALSE)+
geom_point(aes(color=group02),
size=5,
show.legend = TRUE)
ggplot(data=dat,aes(x=x,y=y))+
geom_errorbarh(aes(xmin=x-sd_value,
xmax=x+sd_value,
color=group02),
height=0,
show.legend = FALSE)+
geom_point(aes(color=group02),
size=5,
show.legend = TRUE)+
facet_wrap(~group01)+
theme_bw()+
theme(panel.spacing = unit(0,'lines'),
panel.background = element_blank(),
axis.line = element_line(),
panel.grid = element_blank(),
axis.ticks.y = element_blank(),
strip.text = element_text(hjust = 0))
ggplot(data=dat,aes(x=x,y=y))+
geom_errorbarh(aes(xmin=x-sd_value,
xmax=x+sd_value,
color=group02),
height=0,
show.legend = FALSE)+
geom_point(aes(color=group02),
size=5,
show.legend = TRUE)+
facet_wrap(~group01)+
theme_bw()+
theme(panel.spacing = unit(0,'lines'),
panel.background = element_blank(),
axis.line = element_line(),
panel.grid = element_blank(),
axis.ticks.y = element_blank(),
strip.text = element_text(hjust = 0))+
labs(y="",x=NULL)+
scale_x_continuous(limits = c(-30,30),
breaks = seq(-30,30,10))+
scale_y_continuous(limits = c(0.5,3.5),
breaks = c(1,2,3),
labels=c("SOC concentration",
"SOC stock",
"SOC concentration"),
expand = expansion(mult = c(0,0)))+
geom_vline(xintercept = 0,
color="gray",
lty="dashed")+
geom_hline(yintercept = 1,
color="gray",
lty="dashed")+
geom_hline(yintercept = 2,
color="gray",
lty="dashed")+
geom_hline(yintercept = 3,
color="gray",
lty="dashed") -> p0
p0
p0+
scale_color_manual(values = c(
"A"="#b856d7",
"B"="#55a0fb",
"C"="#0f99b2",
"D"="#ffa040",
"E"="#008000"
),
labels=c(
"A"="Litter addition",
"B"="Litter removal",
"C"="Root removal",
"D"="Litter effect",
"E"="Root effect"
))+
theme(legend.position = "bottom",
legend.title = element_blank()) -> p1
p1
image.png
在这个图的基础上添加注释信息
比如在第一个分面添加一个文本
library(tidyverse)
p1+
annotation_custom2(
data = dat %>% filter(group01=="(a) Litter addition vs. removal"),
grob = grid::textGrob(label="A"),
xmin=-30,xmax=-30,
ymin=0.8,ymax=0.8)
image.png
这个一次性只能添加一个文本，如果文本比较多，可能需要写一个循环
xmin<-c(-30,-30,-30,-30,-30,-30,15,15,15)
xmax<-c(-30,-30,-30,-30,-30,-30,15,15,15)
ymin<-c(0.8,1.2,1.8,2.2,2.8,3.2,1.4,2.4,3.4)
ymax<-c(0.8,1.2,1.8,2.2,2.8,3.2,1.4,2.4,3.4)
label<-c(57,57,23,28,107,116,"p<.001","p<.001","p<.001")
p2<-p1
for (i in 1:9){
p2+
annotation_custom2(
data = dat %>% filter(group01=="(a) Litter addition vs. removal"),
grob = grid::textGrob(label=label[i],hjust=0),
xmin=xmin[i],xmax=xmax[i],
ymin=ymin[i],ymax=ymax[i]) -> p2
}
p2
image.png
在第二个子图和第三个子图添加文本注释也是一样的，这里就不再介绍代码了，可以自己试试
在画图区域外添加文本
p2+
annotation_custom(
#data = dat %>% filter(group01=="(a) Litter addition vs. removal"),
grob = grid::textGrob(label="Percentage change (%)",hjust=0.5),
xmin=0,xmax=0,
ymin=0.28,ymax=0.28)+
coord_cartesian(clip = "off")+
theme(legend.background = element_rect(fill="transparent")) -> p3
p3
image.png
给坐标轴的文本添加背景色
p3+
annotation_custom2(
grob = grid::rectGrob(gp = grid::gpar(fill = '#e2fcf2',
col = '#e2fcf2')),
data = dat %>% filter(group01=="(a) Litter addition vs. removal"),
xmin = -65,
xmax = -33,
ymin = 0.5,
ymax = 1.5)+
annotation_custom2(
grob = grid::rectGrob(gp = grid::gpar(fill = '#ffe9d2',
col = '#ffe9d2')),
data = dat %>% filter(group01=="(a) Litter addition vs. removal"),
xmin = -65,
xmax = -33,
ymin = 1.5,
ymax = 3.5)+
theme(plot.margin = unit(c(0.5,0.5,0.5,5),'lines'))
image.png
最后再添加一些文本信息
p4+
annotation_custom2(
data = dat %>% filter(group01=="(a) Litter addition vs. removal"),
grob = grid::textGrob(label="Data from all\nexperiments with\nthe corresponding treatment",
rot=90,
gp=grid::gpar(col='red')),
xmin=-85,xmax=-85,
ymin=2.5,ymax=2.5)+
annotation_custom2(
data = dat %>% filter(group01=="(a) Litter addition vs. removal"),
grob = grid::textGrob(label="Data from all\nexperiments with\nthe paired treatment",
rot=90,
gp=grid::gpar(col='blue')),
xmin=-85,xmax=-85,
ymin=1,ymax=1)
image.png
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