##############################################soil N figure 8

data <- read.csv("soil N.csv")
df <- data %>% filter(year == 2020)

#2020——NH4_two layer figure 8A
p1 <- ggplot(data=df, aes(x=factor(Date, level=c('2020/8/6', '2020/8/27', '2020/10/3')),y=nh4_1,
                          fill=factor(treatment,level=c('N0', 'N20', 'N60', 'N120', 'N180')))) +
  facet_grid(  ~  layer) +
  geom_bar(position = "dodge", stat="identity",colour = "black",size=0.3)+   
  geom_errorbar(aes(x = Date, y = nh4_1, ymin = nh4_1 - nh4_1_Error, 
                    ymax = nh4_1 + nh4_1_Error),
                width = 0.3,size=0.3,position=position_dodge(.9)) + 
  xlab(expression(paste(Date)))+
  labs(y=expression(~Soil~NH[4]^{"+"}-N~concentration~(mg~kg^{-1})))+
  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'),
        legend.background = element_rect(fill = 'transparent'))+   
  scale_y_continuous(expand = c(0,0),limits = c(0,8)) +  
  labs(fill=' ')+  
  geom_text(label = c("Aa", "Ba", "ABa","Aa", "Ba", 
                      "Acd", "ABab", "Bd", "Abc", "Aa",
                      "Aa", "Aa", "Aa", "Aa", "ABa",
                      "b", "ab", "ab","a", "ab", 
                      "a", "a", "a", "a", "a", 
                      "b", "b", "b", "b", "a"), family="serif",
            aes(y = nh4_1 + nh4_1_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")+
  guides (fill=guide_legend (nrow=1))
p1



#2020——NO3_two layer figure 8B
p2 <- ggplot(data=df, aes(x=factor(Date, level=c('2020/8/6', '2020/8/27', '2020/10/3')),y=no3_1,
                          fill=factor(treatment,level=c('N0', 'N20', 'N60', 'N120', 'N180')))) +
  facet_grid(  ~  layer) +
  geom_bar(position = "dodge", stat="identity",colour = "black",size=0.3)+   
  geom_errorbar(aes(x = Date, y = no3_1, ymin = no3_1 - no3_1_Error, 
                    ymax = no3_1 + no3_1_Error),
                width = 0.3,size=0.3,position=position_dodge(.9)) + 
  xlab(expression(paste(Date)))+
  labs(y=expression(Soil~NO[3]^{"-"}-N~concentration~(mg~kg^{-1})))+
  mytheme2+ 
  theme(legend.position = c(0.06,0.77),
        legend.text = element_text(size = 8, family = "serif"),
        legend.title = element_text( size = 7),
        legend.key.size = unit(0.3, 'cm'),
        legend.background = element_rect(fill = 'transparent'))+   
  scale_y_continuous(expand = c(0,0),limits = c(0,80),breaks=seq(0,80,20)) +  
  geom_text(label = c("b", "ab", "ab","a", "ab", "b", "b", "b", "b", "a", "b", "ab", "ab", "ab", "a",
                      "b", "b", "b","a", "a", "b", "b", "ab", "ab", "a", "a", "a", "a", "a", "a"), family="serif",
            aes(y = no3_1 + no3_1_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



df <- data %>% filter(year == 2021)
data$cut1 = factor(data$cut,levels=c('First regrowth','Second regrowth','Third regrowth'))


#2021——NH4_1two layer figure 8C
p3 <- ggplot(data=df, 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=nh4_1,
                          fill=factor(treatment,level=c('N0', 'N20', 'N60', 'N120', 'N180')))) +
  facet_grid(layer~cut1, 
             scales="free", space="free_x") +
  geom_bar(position = "dodge", stat="identity",colour = "black",size=0.3)+   
  geom_errorbar(aes(x = Date, y = nh4_1, ymin = nh4_1 - nh4_1_Error, 
                    ymax = nh4_1 + nh4_1_Error),
                width = 0.3,size=0.3,position=position_dodge(.9)) + 
  xlab(expression(paste(Date)))+
  labs(y=expression(~Soil~NH[4]^{"+"}-N~concentration~(mg~kg^{-1})))+
  mytheme2+ 
  theme(legend.position = c(0.15, 0.95),
        legend.text = element_text(size = 8, family = "serif"),
        legend.title = element_text( size = 7),
        legend.key.size = unit(0.3, 'cm'),
        legend.background = element_rect(fill = 'transparent'))+   
  scale_y_continuous(expand = c(0,0),limits = c(0,8)) +  
  labs(fill=' ')+  
  geom_text(label = c("Ba", "ABa", "ABa","ABa", "ABa",
                      "ABab", "ABab", "Aa", "ABb", "ABb",
                      "Aa", "Aa", "Aa", "ABab", "ABb",
                      "Aa", "ABab", "ABab","Aa", "BCb", 
                      "ABa", "Ba", "Ba","BCa", "Aa",
                      "ABa", "ABab", "Bb", "ABCb", "ABab",
                      "Ca", "Ca", "Ca","Ca", "Ca",
                      "ABa", "ABa", "ABa","Aa", "ABa", 
                      "ABb", "Aab", "Aab", "Ab", "Aa", 
                      "ABba", "Aa", "Aa","Aa", "ABa",
                      "Aa", "ABa", "ABa","Aa", "Ba", 
                      "Bab", "ABab", "Bb", "Aab", "Aa",
                      "Ba", "ABa", "ABa","Aa", "Ba",
                      "Ca", "Ba", "Ca","Ba", "Ca"), family="serif",
            aes(y = nh4_1 + nh4_1_Error, x = Date), hjust = 0.45,vjust= -0.4, 
            size = 3, position = position_dodge(width = 0.9), stat="identity")+
  theme(panel.spacing.y = unit(1, "lines"))+
  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")
  guides (fill=guide_legend (nrow=1))

p3


##2021—NO3_1two layer  figure 8D
p4 <- ggplot(data=df, 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=no3_1,
                          fill=factor(treatment,level=c('N0', 'N20', 'N60', 'N120', 'N180')))) +
  facet_grid(layer~cut1, 
             scales="free", space="free_x") +
  geom_bar(position = "dodge", stat="identity",colour = "black",size=0.3)+   
  geom_errorbar(aes(x = Date, y = no3_1, ymin = no3_1 - no3_1_Error, 
                    ymax = no3_1 + no3_1_Error),
                width = 0.3,size=0.3,position=position_dodge(.9)) + 
  xlab(expression(paste(Date)))+
  labs(y=expression(Soil~NO[3]^{"-"}-N~concentration~(mg~kg^{-1})))+
  mytheme2+ 
  theme(legend.position = c(0.05,0.86),
        legend.text = element_text(size = 8, family = "serif"),
        legend.title = element_text( size = 7),
        legend.key.size = unit(0.3, 'cm'),
        legend.background = element_rect(fill = 'transparent'))+   
  scale_y_continuous(expand = c(0,0),limits = c(0,80),breaks=seq(0,80,20)) +  
  labs(fill=' ')+  
  geom_text(label = c("Aa", "Aa", "Aa","ABa", "ABa", 
                      "Ab", "Ab", "Ab", "Aab", "Aa", 
                      "Ab", "Ab", "Ab", "ABb", "ABa",
                      "Aa", "Aa", "Aa","ABa", "ABa",
                      "Ab", "Aab", "Bab", "Bab", "Ba",
                      "Aa", "Aa", "Ba","Ba", "Ba",
                      "Aa", "Aa", "Ba","Ba", "Ba",
                      "b", "ab", "ab","a", "a", "a", "a", "a", "a", "a", "b", "b", "b", "b", "a",
                      "a", "a", "a", "a", "a",  "a", "a", "a", "a", "a", "b", "b", "a", "a", "ab",
                      "a", "a", "a", "a", "a"), family="serif",
            aes(y = no3_1 + no3_1_Error, x = Date), hjust = 0.45,vjust= -0.4, 
            size = 3, position = position_dodge(width = 0.9), stat="identity")+
  theme(panel.spacing.y = unit(1, "lines"))+
  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")
p4


plot_all <- cowplot::plot_grid(p1, p2,p3,p4, 
                               labels = "AUTO",label_fontfamily="serif",nrow = 4,rel_heights = c (1.5, 1.5,2,2))
plot_all


ggsave("paper_soil_c.png", plot=plot_all,
       height=35, width=25, units="cm", dpi=600)