library(gridExtra)

GrCh.data<-read.csv(file="/Users/ryokooono/Dropbox/R_codes_datasets/LegumeRhizobiaDataset/Growth_chamber_Fall2016_v2.csv")

GrCh.rhizobia <- GrCh.data[-which(GrCh.data$Strain_trt =="Control" & GrCh.data$Total_nodule_wt>0.05),]
GrCh.root <-na.omit(GrCh.rhizobia[,c("Nitrogen_trt","Strain_trt","root_wt")])


df_root_wt <- summarySE(GrCh.rhizobia, measurevar="root_wt", na.rm=TRUE,
                         groupvars=c("Nitrogen_trt", "Strain_trt"))
# Convert dose to a factor variable
df_root_wt$Nitrogen_trt=as.factor(df_root_wt$Nitrogen_trt)
df_root_wt$Strain_trt=as.factor(df_root_wt$Strain_trt)
df_root_wt$Nitrogen_trt <- factor(df_root_wt$Nitrogen_trt, levels = c("none","low","high"  ))
df_root_wt$Strain_trt <- factor(df_root_wt$Strain_trt, levels = c("Control", "CE3", "Mix", "SAM100"))

df_root_wt<-df_root_wt[c(10,6,2, 9,5,1, 11,7,3, 12,8,4),]


GC_root_wt_aov<-aov(GrCh.root$root_wt~GrCh.root$Nitrogen_trt*GrCh.root$Strain_trt)

summary(GC_root_wt_aov)
capture.output(summary(GC_root_wt_aov),file="/Users/ryokooono/Dropbox/R_figures/LegumeRhizobia/root_anova.doc")

GC_root_HSD <- TukeyHSD(x=GC_root_wt_aov)


GC_root.levels <- GC_root_HSD$'GrCh.root$Nitrogen_trt:GrCh.root$Strain_trt'[,4]
GC_root.labels <- data.frame(multcompLetters(GC_root.levels)['Letters'])
GC_root.labels$treatment=rownames(GC_root.labels)
#GC_root.labels=GC_root.labels[c(5,4,3,2,1,12,8,7,6,11,10,9) , ]

#df_root_wt$TukeyLetter <-GC_root.labels$Letters
#df_root_wt$y <-c(0.28,0.18,0.24, 0.22,0.21,0.25, 0.22,0.23,0.25, 0.22,0.23,0.27)

#df_root_wt$N_treatment <- factor(df_root_wt$N_treatment, levels = c("none", "5mM"))
#df_root_wt$x <- c(0.7,1,1.3, 1.7,2,2.3, 2.7,3,3.3, 3.7,4,4.3)



rootWt_GC <- ggplot(df_root_wt, aes(x = Strain_trt, y = -root_wt, fill = Nitrogen_trt)) +   
  geom_bar(position = position_dodge(), stat="identity", colour="black") +
  geom_errorbar(aes(ymin=-root_wt-se, ymax=-root_wt+se), width=.2,
                position=position_dodge(.9)) + theme_bw() +
  scale_fill_manual(values = c("white","lightgrey", "darkgrey"), name = "",
                    labels = c("No nitrate","1 mM nitrate", "5 mM nitrate")) +
  theme(axis.text.x=element_blank(), axis.text.y=element_text(size=14), 
        legend.text=element_text(size=14), axis.title =element_text(size=14),
        legend.position = "bottom",
        panel.grid.major = element_blank(),
        panel.grid.minor = element_blank(),
        panel.border = element_blank(),
        axis.line = element_line(colour = "black"),
        legend.title=element_text(size=14),
  plot.margin = margin(-90, 5.5, 5.5, 5.5, "pt")) +
  scale_x_discrete(position = "top") +
  scale_y_continuous(breaks = c(-0.2,-0.1,0), 
                     labels = c("0.2","0.1","0")) +
  xlab("") +
  ylab("Root dry weight (g)") 
 # geom_text(size = 4,mapping = aes(x = x, y = -y, label = TukeyLetter, fill = NULL)) 



png('/Users/ryokooono/Dropbox/R_figures/LegumeRhizobia/GC_shoot_root.png', units="in", width=5, height=6, res=300)
grid.arrange(shootWt_GC, rootWt_GC, ncol = 1,heights =c(2,0.6))
dev.off()