##################################################################Figure 2

df<- read.csv("2_field.csv")

data<-df%>% filter(year== "2020")

##########Figure 2 A

#2020 height
p1 <- ggplot(data=data, aes(x=factor(Date, level=c('2020/8/6', '2020/8/27', '2020/10/3')),y=height,
                            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 = height, ymin = height - height_error, 
                    ymax = height + height_error),
                width = 0.3,size=0.3,position=position_dodge(.9)) + 
  xlab(expression(paste(Date)))+
  labs(y=expression(Height~(cm)))+
  mytheme2+ 
  theme(legend.position = c(0.15,0.80),
        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)) +  
  scale_x_discrete()+ # 字符
  geom_text(label = c("a", "a", "a","a", "a", "a", "a", "a", "a", "a", "a", "a", "a", "a", "a"), family="serif",
            aes(y = height + height_error, x = Date), hjust = 0.45,vjust= -0.4, 
            size = 3, position = position_dodge(width = 0.9), stat="identity")+#加显著性字母并调整位置
  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", "right", "bottom", "top")+
p1




#2020 stem diameter Figure 2C
p2 <- ggplot(data=data, aes(x=factor(Date, level=c('2020/8/6', '2020/8/27', '2020/10/3')),y=stem_diameter,
                            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 = stem_diameter, ymin = stem_diameter - stem_diameter_error, 
                    ymax = stem_diameter + stem_diameter_error),
                width = 0.3,size=0.3,position=position_dodge(.9))+
  xlab(expression(paste(Date)))+
  labs(y=expression(Stem~diameter~(mm)))+
  mytheme2+ 
  theme(legend.position = c(0.15,0.80),
        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)) +
  scale_fill_manual( values = c("#00AFBB", "#E7B800", "#FC4E07","cornflowerblue","violet"),name = NULL)+
  geom_text(label = c("a", "a", "a","a", "a", "a", "a", "a", "a", "a", "a", "a", "a", "a", "a"), family="serif",
            aes(y = stem_diameter + stem_diameter_error, x = Date), hjust = 0.45,vjust= -0.4, size = 3, 
            position = position_dodge(width = 0.9), stat="identity")+
  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", "right", "bottom", "top")

p2


#2020 branch number Figure 2E
p3 <- ggplot(data=data, aes(x=factor(Date, level=c('2020/8/6', '2020/8/27', '2020/10/3')),y=branchingnumber,
                            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 = branchingnumber, ymin = branchingnumber - branchingnumber_error, 
                    ymax = branchingnumber + branchingnumber_error),
                width = 0.3,size=0.3,position=position_dodge(.9)) +
  xlab(expression(paste(Date)))+
  labs(y=expression(Branching~number~(branch~plant^{-1})))+
  geom_text(label = c("a", "a", "a","a", "a", "a", "a", "a", "a", "a", "a", "a", "a", "a", "a"),  family="serif",
            aes(y = branchingnumber + branchingnumber_error, x = Date), hjust = 0.45,vjust= -0.4, size = 3, position = position_dodge(width = 0.9), stat="identity")+#加显著性字母并调整位置
  scale_fill_manual( values = c("#00AFBB", "#E7B800", "#FC4E07","cornflowerblue","violet"),name = NULL)+
  mytheme2+ 
  theme(legend.position = c(0.15,0.80),
        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(0,20)) +
  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", "right", "bottom", "top")

p3


###2021 height  Figure 2B

df<- read.csv("2_field.csv")
data<-df%>% filter(year== "2021")

data$cut1 = factor(data$cut, levels=c('First regrowth','Second regrowth','Third regrowth'))
p4 <- 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=height, 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 = height, ymin = height - height_error, 
                    ymax = height + height_error),
                width = 0.3,size=0.3,position=position_dodge(.9)) +
  xlab(expression(paste(Date)))+
  labs(y=expression(Height~(cm)))+
  mytheme2+ 
  theme(legend.position = c(0.08,0.82),
        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(0,120)) +
  labs(fill=' ')+  
  geom_text(label = c("b", "b", "ab","a", "a", "ab", "b", "ab", "ab", "a", "a", "a", "a", "a", "a",
                      "a", "a", "a","a", "a", "a", "a", "a", "a", "a", "a", "a", "a", "a", "a",
                      "a", "a", "a","a", "a"), family="serif",
            aes(y = height + height_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)+
  labs(fill=' ')+  
  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", "right", "bottom", "top")
p4





#stem diameter  Figure 2D
df<- read.csv("2_field.csv")
data<-df%>% filter(year== "2021")

data$cut1 = factor(data$cut, levels=c('First regrowth','Second regrowth','Third regrowth'))
p5 <-   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=stem_diameter, fill=factor(treatment,level=c('N0', 'N20', 'N60', 'N120', 'N180')))) +#调整X轴顺序
  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 = stem_diameter, ymin = stem_diameter - stem_diameter_error, 
                    ymax = stem_diameter + stem_diameter_error),
                width = 0.3,size=0.3,position=position_dodge(.9))+
  xlab(expression(paste(Date)))+
  labs(y=expression(Stem~diameter~(mm)))+
  mytheme2+ 
  theme(legend.position = c(0.06,0.85),
        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(0,6)) +
  labs(fill=' ')+  
  geom_text(label = c("b", "b", "ab","a", "a", "ab", "b", "ab", "ab", "a", "a", "a", "a", "a", "a",
                      "a", "a", "a", "a", "a", "a", "a", "a", "a", "a","a", "a", "a", "a", "a",
                      "a", "a", "a", "a", "a"), family="serif",
            aes(y = stem_diameter + stem_diameter_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)+
  labs(fill=' ')+  
  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", "right", "bottom", "top")
p5



#2021 branch number  Figure 2F
df<- read.csv("2_field.csv")
data<-df%>% filter(year== "2021")

data$cut1 = factor(data$cut, levels=c('First regrowth','Second regrowth','Third regrowth'))
p6 <-    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=branchingnumber, 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 = branchingnumber, ymin = branchingnumber - branchingnumber_error, 
                    ymax = branchingnumber + branchingnumber_error),
                width = 0.3,size=0.3,position=position_dodge(.9)) +
  xlab(expression(paste(Date)))+
  labs(y=expression(Branching~number~(branch~plant^{-1})))+
  mytheme2+ 
  theme(legend.position = c(0.08,0.82),
        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(0,20)) +
  labs(fill=' ')+
  geom_text(label = c("a", "a", "a", "a", "a", "b", "ab", "a", "ab", "a", "b", "ab", "a", "a", "a",
                      "a", "a", "a", "a", "a", "b", "ab", "ab", "a", "ab", "a", "a", "a", "a", "a",
                      "a", "a", "a", "a", "a"), family="serif",
            aes(y =  branchingnumber + branchingnumber_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)+
  labs(fill=' ')+
  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")
p6

########## alfalfa growth

############################
plot_height <- cowplot::plot_grid(p1,p4,labels = c("A","B"),label_fontfamily="serif",rel_widths = c (1, 2))
plot_height 

plot_stem <- cowplot::plot_grid(p2,p5,labels = c("C","D"),label_fontfamily="serif",rel_widths = c (1, 2))
plot_stem 

plot_branch <- cowplot::plot_grid(p3,p6,labels = c("E","F"),label_fontfamily="serif",rel_widths = c (1, 2))
plot_branch 
plot_all <- cowplot::plot_grid(plot_height, plot_stem, plot_branch ,labels = NULL,nrow=3)

plot_all


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