########################################################################### figure 5
################### leaf concentration 

#2020 figure 5A
df<- read.csv("2_field.csv")
data<-df%>% filter(year== "2020")

p1 <- ggplot(data=data, aes(x=factor(Date, level=c('2020/8/6', '2020/8/27', '2020/10/3')),y=leafN_concerntration,
                            fill=factor(treatment,level=c('N0', 'N20', 'N60', 'N120', 'N180')))) +
  geom_bar(position = "dodge", stat="identity",colour = "black",size=0.3)+   
  geom_errorbar(aes(x = Date, y = leafN_concerntration, ymin = leafN_concerntration - leafN_concerntration_error, 
                    ymax = leafN_concerntration + leafN_concerntration_error),
                width = 0.3,size=0.3,position=position_dodge(.9)) + 
  xlab(expression(paste(Date)))+
  labs(y=expression(Leaf~N~concentration~("%")))+
  mytheme2+ 
  theme(legend.position = c(0.15, 0.85),
        legend.text = element_text(size = 8, family = "serif"),
        legend.title = element_text( size = 7),
        legend.key.size = unit(0.3, 'cm'))+   
  scale_y_continuous(expand = c(0,0),limits = c(0,10)) +  
  labs(fill=' ')+  
  geom_text(label = c("b", "ab", "ab","a", "ab", "b", "a", "a", "a", "a", "b", "a", "ab", "ab", "ab"), family="serif",
            aes(y = leafN_concerntration + leafN_concerntration_error, x = Date), hjust = 0.45,vjust= -0.4, 
            size = 3, position = position_dodge(width = 0.9), stat="identity")+
  scale_fill_manual( values = c("#00AFBB", "#E7B800", "#FC4E07","cornflowerblue","violet"),name = NULL)+
  theme(
    axis.title.y = element_text(vjust = 3,margin = margin(t =0, r = 0, b = 0, l = 0)),
    axis.title.x = element_text(vjust = -1,margin = margin(t =0, r = 0, b = 0, l = 0)))+
  theme(plot.margin = unit(c(1,1,0.5,1), "cm")) # ("left", "top", "bottom", "right")
p1


#2021 figure 5B
data<-df%>% filter(year== "2021")
data$cut1 = factor(data$cut, levels=c('First regrowth','Second regrowth','Third regrowth'))
p2 <-    ggplot(data=data, aes(x=factor(Date, level=c('2021/5/26', '2021/6/3', '2021/6/15', 
                                                      '2021/7/16','2021/7/30','2021/8/7','2021/9/24')),y=leafN_concerntration,
                               fill=factor(treatment,level=c('N0', 'N20', 'N60', 'N120', 'N180')))) +
  facet_grid(. ~cut1,
             scales="free_x",
             space = "free") +  
  geom_bar(position = "dodge", stat="identity",colour = "black",size=0.3)+   
  geom_errorbar(aes(x = Date, y = leafN_concerntration, ymin = leafN_concerntration - leafN_concerntration_error, 
                    ymax = leafN_concerntration + leafN_concerntration_error),
                width = 0.3,size=0.3,position=position_dodge(.9)) + 
  xlab(expression(paste(Date)))+
  labs(y=expression(Leaf~N~concentration~("%")))+
  mytheme2+ 
  theme(legend.position = c(0.08, 0.86),
        legend.text = element_text(size = 8, family = "serif"),
        legend.title = element_text( size = 7),
        legend.key.size = unit(0.3, 'cm'))+   
  scale_y_continuous(expand = c(0,0),limits = c(0,10)) +  
  labs(fill=' ')+  
  geom_text(label = c("b", "ab", "ab","a", "b", "ab", "ab", "a", "b", "b", "a", "a", "a", "a", "a",
                      "b", "ab", "a","a", "a", "a", "a", "a", "a", "a", "a", "a", "a", "a", "a",
                      "a", "a", "a", "a", "a"), family="serif",
            aes(y = leafN_concerntration + leafN_concerntration_error, x = Date), hjust = 0.45,vjust= -0.4, 
            size = 3, position = position_dodge(width = 0.9), stat="identity")+
  scale_fill_manual( values = c("#00AFBB", "#E7B800", "#FC4E07","cornflowerblue","violet"),name = NULL)+
  theme(
    axis.title.y = element_text(vjust = 3,margin = margin(t =0, r = 0, b = 0, l = 0)),
    axis.title.x = element_text(vjust = -1,margin = margin(t =0, r = 0, b = 0, l = 0)))+
  theme(plot.margin = unit(c(1,1,0.5,1), "cm")) # ("left", "top", "bottom", "right")


p2

LEAF <- cowplot::plot_grid(p1, p2, labels = "AUTO",label_fontfamily="serif",nrow = 1,rel_widths = c (1,2))

LEAF


#############################stem n concentration

#2020 figure 5C
data<-df%>% filter(year== "2020")
p1 <- ggplot(data=data, aes(x=factor(Date, level=c('2020/8/6', '2020/8/27', '2020/10/3')),y=stemN_concerntration,
                            fill=factor(treatment,level=c('N0', 'N20', 'N60', 'N120', 'N180')))) +
  geom_bar(position = "dodge", stat="identity",colour = "black",size=0.3)+   
  geom_errorbar(aes(x = Date, y = stemN_concerntration, ymin = stemN_concerntration - stemN_concerntration_error, 
                    ymax = stemN_concerntration + stemN_concerntration_error),
                width = 0.3,size=0.3,position=position_dodge(.9)) + 
  xlab(expression(paste(Date)))+
  labs(y=expression(Stem~N~concentration~("%")))+
  mytheme2+ 
  theme(legend.position = c(0.15, 0.88),
        legend.text = element_text(size = 8, family = "serif"),
        legend.title = element_text( size = 7),
        legend.key.size = unit(0.3, 'cm'))+   
  scale_y_continuous(expand = c(0,0),limits = c(0,4)) +  
  labs(fill=' ')+  
  geom_text(label = c("c", "bc", "ab","ab", "a", "a", "a", "a", "a", "a", "a", "a", "a", "a", "a"), family="serif",
            aes(y = stemN_concerntration + stemN_concerntration_error, x = Date), hjust = 0.45,vjust= -0.4, 
            size = 3, position = position_dodge(width = 0.9), stat="identity")+
  scale_fill_manual( values = c("#00AFBB", "#E7B800", "#FC4E07","cornflowerblue","violet"),name = NULL)+
  theme(
    axis.title.y = element_text(vjust = 3,margin = margin(t =0, r =0, b = 0, l = 0)),
    axis.title.x = element_text(vjust = -1,margin = margin(t =0, r = 0, b = 0, l = 0)))+
  theme(plot.margin = unit(c(1,1,0.5,1), "cm")) # ("left", "top", "bottom", "right")



p1


#2021 figure 5D

data<-df%>% filter(year== "2021")
data$cut1 = factor(data$cut, levels=c('First regrowth','Second regrowth','Third regrowth'))
p2 <-    ggplot(data=data, aes(x=factor(Date, level=c('2021/5/26', '2021/6/3', '2021/6/15', 
                                                      '2021/7/16','2021/7/30','2021/8/7','2021/9/24')),y=stemN_concerntration,
                               fill=factor(treatment,level=c('N0', 'N20', 'N60', 'N120', 'N180')))) +
  facet_grid(. ~cut1,
             scales="free_x",
             space = "free") +  
  geom_bar(position = "dodge", stat="identity",colour = "black",size=0.3)+   
  geom_errorbar(aes(x = Date, y = stemN_concerntration, ymin = stemN_concerntration - stemN_concerntration_error, 
                    ymax = stemN_concerntration + stemN_concerntration_error),
                width = 0.3,size=0.3,position=position_dodge(.9)) + 
  xlab(expression(paste(Date)))+
  labs(y=expression(Stem~N~concentration~("%")))+
  mytheme2+ 
  theme(legend.position = c(0.05, 0.88),
        legend.text = element_text(size = 8, family = "serif"),
        legend.title = element_text( size = 7),
        legend.key.size = unit(0.3, 'cm'))+   
  scale_y_continuous(expand = c(0,0),limits = c(0,4)) +  
  labs(fill=' ')+  
  geom_text(label = c("a", "a", "a","a", "a", "a", "a", "ab", "a", "b", "a", "a", "a", "a", "a",
                      "a", "a", "a","a", "a", "a", "a", "a", "a", "a", "ab", "a", "a", "ab", "b",
                      "a", "a", "a","a", "a"), family="serif",
            aes(y = stemN_concerntration + stemN_concerntration_error, x = Date), hjust = 0.45,vjust= -0.4, 
            size = 3, position = position_dodge(width = 0.9), stat="identity")+
  scale_fill_manual( values = c("#00AFBB", "#E7B800", "#FC4E07","cornflowerblue","violet"),name = NULL)+
  theme(
    axis.title.y = element_text(vjust = 3,margin = margin(t =0, r = 0, b = 0, l = 0)),
    axis.title.x = element_text(vjust = -1,margin = margin(t =0, r = 0, b = 0, l = 0)))+
  theme(plot.margin = unit(c(1,1,0.5,1), "cm")) # ("left", "top", "bottom", "right")
p2
##########hebing
STEM <- cowplot::plot_grid(p1, p2, labels = c("C","D"),label_fontfamily="serif",nrow = 1,rel_widths = c (1,2))

STEM



#2020 root figure 5E
data<-df%>% filter(year== "2020")
p1 <- ggplot(data=data, aes(x=factor(Date, level=c('2020/8/6', '2020/8/27', '2020/10/3')),y=rootN_concentration,
                            fill=factor(treatment,level=c('N0', 'N20', 'N60', 'N120', 'N180')))) +
  geom_bar(position = "dodge", stat="identity",colour = "black",size=0.3)+   
  geom_errorbar(aes(x = Date, y = rootN_concentration, ymin = rootN_concentration - rootN_concentration_error, 
                    ymax = rootN_concentration + rootN_concentration_error),
                width = 0.3,size=0.3,position=position_dodge(.9)) + 
  xlab(expression(paste(Date)))+
  labs(y=expression(Root~N~concentration~("%")))+
  mytheme2+ 
  theme(legend.position = c(0.15, 0.85),
        legend.text = element_text(size = 8, family = "serif"),
        legend.title = element_text( size = 7),
        legend.key.size = unit(0.3, 'cm'))+   小
scale_y_continuous(expand = c(0,0),limits = c(0,4)) +  
  labs(fill=' ')+  
  geom_text(label = c("b", "a", "a","a", "a", "b", "ab", "ab", "a", "a",  "a", "a", "a", "a", "a"), family="serif",
            aes(y = rootN_concentration + rootN_concentration_error, x = Date), hjust = 0.45,vjust= -0.4, 
            size = 3, position = position_dodge(width = 0.9), stat="identity")+
  scale_fill_manual( values = c("#00AFBB", "#E7B800", "#FC4E07","cornflowerblue","violet"),name = NULL)+
  theme(
    axis.title.y = element_text(vjust = 3,margin = margin(t =0, r = 0, b = 0, l = 0)),
    axis.title.x = element_text(vjust = -1,margin = margin(t =0, r = 0, b = 0, l = 0)))+
  theme(plot.margin = unit(c(1,1,0.5,1), "cm")) # ("left", "top", "bottom", "right"
p1

##################################root concentration
# root figure 5F
data<-df%>% filter(year== "2021")
data$cut1 = factor(data$cut, levels=c('First regrowth','Second regrowth','Third regrowth'))
p2 <-    ggplot(data=data, aes(x=factor(Date, level=c('2021/5/26', '2021/6/3', '2021/6/15', 
                                                      '2021/7/16','2021/7/30','2021/8/7','2021/9/24')),y=rootN_concentration,
                               fill=factor(treatment,level=c('N0', 'N20', 'N60', 'N120', 'N180')))) +
  facet_grid(. ~cut1,
             scales="free_x",
             space = "free") +
  geom_bar(position = "dodge", stat="identity",colour = "black",size=0.3)+   
  geom_errorbar(aes(x = Date, y = rootN_concentration, ymin = rootN_concentration - rootN_concentration_error, 
                    ymax = rootN_concentration + rootN_concentration_error),
                width = 0.3,size=0.3,position=position_dodge(.9)) + 
  xlab(expression(paste(Date)))+
  labs(y=expression(Root~N~concentration~("%")))+
  mytheme2+ 
  theme(legend.position = c(0.08, 0.87),
        legend.text = element_text(size = 8, family = "serif"),
        legend.title = element_text( size = 7),
        legend.key.size = unit(0.3, 'cm'))+   
  scale_y_continuous(expand = c(0,0),limits = c(0,4)) +  
  labs(fill=' ')+  
  geom_text(label = c("b", "ab", "a","a", "a", "b", "ab", "ab", "a", "a","a", "a", "a", "a", "a",
                      "b", "a", "a","a", "a", "b", "ab", "ab", "a", "a", "a", "a", "a", "a", "a",
                      "a", "a", "a", "a", "a"),family="serif", 
            aes(y = rootN_concentration + rootN_concentration_error, x = Date), hjust = 0.45,vjust= -0.4, 
            size = 3, position = position_dodge(width = 0.9), stat="identity")+
  scale_fill_manual( values = c("#00AFBB", "#E7B800", "#FC4E07","cornflowerblue","violet"),name = NULL)+
  theme(
    axis.title.y = element_text(vjust = 3,margin = margin(t =0, r = 0, b = 0, l = 0)),
    axis.title.x = element_text(vjust = -1,margin = margin(t =0, r = 0, b = 0, l = 0)))+
  theme(plot.margin = unit(c(1,1,0.5,1), "cm")) # ("left", "top", "bottom", "right")
p2

##########
ROOT <- cowplot::plot_grid(p1, p2, labels = c("E","F"),label_fontfamily="serif",nrow = 1,rel_widths = c (1,2))

ROOT

plot_all <- cowplot::plot_grid(LEAF, STEM, ROOT,labels = NULL,label_fontfamily="serif",nrow = 3)

plot_all

ggsave("paper_all_con_c.png", plot=plot_all,
       height=30, width=25, units="cm", dpi=600)