R Script for GGE plot

library(metan) 
library(tidyverse) 

############A basic biplot 
gge_model <- gge(stability, ENV, GEN, C1) 
a <- plot(gge_model) 

C1 <- plot(gge_model, 
           col.gen = "red", 
           size.text.env = 3, 
           axis_expand = 1, 
           plot_theme = theme_metan(grid = "both")) 

arrange_ggplot(GNPS, tag_levels = "a") + theme_bw() 

##############Mean performance vs. stability 
gge_model <- gge(stability, ENV, GEN, C1, svp = "genotype") 
c <- plot(gge_model, type = 2) 

d <- plot(gge_model, 
          type = 2, 
          col.gen = "blue", 
          col.env = "red", 
          axis_expand = 1, 
          plot_theme = theme_metan_minimal()) 

arrange_ggplot(d, tag_levels = list(c("c", "d"))) 

######################################Which-won-where 
gge_model <- gge(stability, ENV, GEN, C1, svp = "symmetrical") 
e <- plot(gge_model, type = 3) 

f <- plot(gge_model, 
          type = 3, 
          size.shape.win = 5, 
          large_label = 6, 
          col.gen = "blue", 
          col.env = "black", 
          axis_expand = 1, 
          title = FALSE) 

arrange_ggplot(f, tag_levels = list(c("e", "f"))) + theme_bw() 

#########################Discriminativeness vs. representativeness 
g <- plot(gge_model, type = 4) 

h <- plot(gge_model, 
          type = 4, 
          plot_theme = theme_metan_minimal()) 

arrange_ggplot(h, tag_levels = list(c("g", "h"))) 

###########################3Ranking environments 
gge_model <- gge(stability, ENV, GEN, C1) 
k <- plot(gge_model, type = 6) 

l <- plot(gge_model, 
          type = 6, 
          col.gen = "black", 
          col.env = "blue", 
          col.circle = "red", 
          col.alpha.circle = 0.5, 
          size.text.env = 5, 
          axis_expand = 1.5, 
          plot_theme = theme_metan(color.background = "white")) 

arrange_ggplot(l, tag_levels = list(c("k", "l"))) 

#######################################Ranking genotypes 
o <- plot(gge_model, type = 8) 

p <- plot(gge_model, 
          type = 8, 
          col.gen = "blue", 
          col.env = "black", 
          size.text.gen = 6, 
          plot_theme = theme_metan_minimal()) 

arrange_ggplot(p, tag_levels = list(c("o", "p"))) 

########################################Relationship among environments 
gge_model <- gge(stability, ENV, GEN, C1) 
s <- plot(gge_model, type = 10) 

t <- plot(gge_model, 
          type = 10, 
          col.gen = "black", 
          title = FALSE) 

arrange_ggplot(t, tag_levels = list(c("s", "t"))) + theme_bw()