###################################################################figure 7
###############################alfalfa cp
#2020 CP figure 7A
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=CP,
                            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 = CP, ymin = CP - CP_error, 
                    ymax = CP + CP_error),
                width = 0.3,size=0.3,position=position_dodge(.9)) + 
  xlab(expression(paste(Date)))+
  labs(y=expression(Alfalfa~Crude~Protein~("%")))+
  mytheme2+ 
  theme(legend.position = c(0.85, 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(0,40)) +  
  geom_text(label = c("Ab", "Aab", "Aab","Aa", "Aa", 
                      "Ac", "Aab", "Aa", "ABbc", "ABabc", 
                      "Ab", "Aa", "Aab", "Bab", "Bab"), family="serif",
            aes(y = CP + CP_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 CP figure 7B
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=CP,
                               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 = CP, ymin = CP - CP_error, 
                    ymax = CP + CP_error),
                width = 0.3,size=0.3,position=position_dodge(.9)) + 
  xlab(expression(paste(Date)))+
  labs(y=expression(Alfalfa~Crude~Protein~("%")))+
  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(0,40)) +  
  geom_text(label = c("ABb", "Ab", "ABab","ABa", "ABab", 
                      "Cab", "Ba", "Cab", "Cab", "Cb", 
                      "Da", "Ca", "Da", "Da", "Da",
                      "Ab", "Aab", "Aa","Aa", "Aab",
                      "ABb","Aab","ABa","ABa","Aa", 
                      "BCa", "Ba", "BCa", "Ca", "BCa",
                      "Aa", "Aa", "Ba", "ABa", "Aa"), family="serif",
            aes(y = CP + CP_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

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


##############################################alfalfa ADF
#2020ADF figure 7C
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=ADF,
                            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 = ADF, ymin = ADF - ADF_error, 
                    ymax = ADF + ADF_error),
                width = 0.3,size=0.3,position=position_dodge(.9)) + 
  xlab(expression(paste(Date)))+
  labs(y=expression(Alfalfa~Acid~Detergent~Fiber~("%")))+
  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(0,60)) +  
  geom_text(label = c("ab", "ab", "ab","b", "a", "a", "a", "a", "a", "a", "a", "bc", "ab", "c", "a", "ab"), family="serif",
            aes(y = ADF + ADF_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

#2021ADF figure 7D
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=ADF,
                               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 = ADF, ymin = ADF - ADF_error, 
                    ymax = ADF + ADF_error),
                width = 0.3,size=0.3,position=position_dodge(.9)) + 
  xlab(expression(paste(Date)))+
  labs(y=expression(Alfalfa~Acid~Detergent~Fiber~("%")))+
  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(0,60)) +  
  labs(fill=' ')+  
  geom_text(label = c("a", "ab", "ab","b", "ab", "a", "a", "a", "a", "a", "a", "a", "a", "a", "a",
                      "a", "ab", "b","ab", "ab",  "a", "a", "a", "a", "a", "a", "a", "a", "a", "a",
                      "a", "a", "a", "a", "a"), family="serif",
            aes(y = ADF + ADF_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

##########
ADF<- cowplot::plot_grid(p1, p2, labels = c("C","D"),label_fontfamily="serif",nrow = 1,rel_widths = c (1, 2))



#########################################alfalfa NDF
#2020NDF figure 7E
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=NDF,
                            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 = NDF, ymin = NDF - NDF_error, 
                    ymax = NDF + NDF_error),
                width = 0.3,size=0.3,position=position_dodge(.9)) + 
  xlab(expression(paste(Date)))+
  labs(y=expression(Alfalfa~Neutral~Detergent~Fiber~("%")))+
  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(0,80),breaks =  seq(0,80,20)) +  
  geom_text(label = c("a", "a", "a","a", "a", "a", "a", "a", "a", "a", "a", "a", "a", "a", "a"), family="serif", 
            aes(y = NDF + NDF_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


######2021NDF figure 7F
#NDF
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=NDF,
                               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 = NDF, ymin = NDF - NDF_error, 
                    ymax = NDF + NDF_error),
                width = 0.3,size=0.3,position=position_dodge(.9)) + 
  xlab(expression(paste(Date)))+
  labs(y=expression(Alfalfa~Neutral~Detergent~Fiber~("%")))+
  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(0,80)) +  
  labs(fill=' ')+  
  geom_text(label = c("a", "ab", "ab","b", "ab",  "a", "a", "a", "a", "a",  "a", "a", "a", "a", "a",
                      "a", "ab", "b","ab", "ab",  "a", "a", "a", "a", "a",  "a", "a", "a", "a", "a",
                      "a", "a", "a", "a", "a"), family="serif",
            aes(y = NDF + NDF_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

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

NDF

plot_all <- cowplot::plot_grid(cp, ADF,NDF, labels = NULL,label_fontfamily="serif",nrow = 3)

plot_all

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