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gg_Volcano()

Source: vignettes/gg_Volcano.Rmd
gg_Volcano.Rmd

The function gg_Volcano() creates volcano plots from GAPIT GWAS results.

Specifying a folder and trait is all that is needed to create manhattan plots.

# Plot
mp <- gg_Volcano(
  # Specify a folder with GWAS results
  folder = "GWAS_Results/", 
  # Select a trait to plot
  trait = "DTF_Nepal_2017" )
# Save
ggsave("figures/gg_Volcano_01.png", mp, width = 12, height = 4)

Customized Plot 

# Plot
mp <- gg_Volcano(
  # Specify a folder with GWAS results
  folder = "GWAS_Results/", 
  # Select a trait to plot
  trait = "DTF_Nepal_2017",
  # Plot only certain GWAS models
  models = c("MLM","MLMM","FarmCPU","BLINK"),
  # Highlight specific markers
  markers = c("Lcu.1GRN.Chr2p44545877", 
              "Lcu.1GRN.Chr5p1658484"), 
  # Create alt labels for the markers
  labels = c("44545877","1658484") 
  )
# Save
ggsave("figures/gg_Volcano_02.png", mp, width = 12, height = 4)