Skip to contents

gg_Manhattan_xModels()

2.4_gg_Manhattan_xModels.Rmd

The function gg_Manhattan_xModels() creates manhattan plots from GAPIT GWAS results for multiple traits and facets them by Model. This allows the user to compare the results from different traits across each GWAS model.

Specifying a folder and traits is all that is needed to create manhattan plots for multiple traits.

# Plot
mp <- gg_Manhattan_xModels(
  # Specify a folder with GWAS results
  folder = "GWAS_Results/",
  # Select traits to plot
  traits = c("DTF_Nepal_2017", "DTF_Sask_2017", "DTF_Sask_2017_b") )
# Save
ggsave("figures/gg_Manhattan_xModels_01.png", mp, width = 12, height = 8, bg = "white")

Customized Plot 

# Plot
mp <- gg_Manhattan_xModels(
  # Specify a folder with GWAS results
  folder = "GWAS_Results/",
  # Select traits to plot
  traits = c("DTF_Nepal_2017", "DTF_Sask_2017", "DTF_Sask_2017_b"),
  # Specify a title
  title = "Days to Flower",
  # Add vertical lines
  vlines = c("Lcu.1GRN.Chr2p44545877",
              "Lcu.1GRN.Chr5p1658484",
              "Lcu.1GRN.Chr6p3269280"),
  vline.colors = c("red", "red", "blue"),
  vline.types = c(2,2,1),
  # Change the legend alignment
  legend.box="vertical",
  # Choose a GWAS model
  models =  c("MLM","MLMM","FarmCPU","BLINK") )
# Save
ggsave("figures/gg_Manhattan_xModels_02.png", mp, width = 12, height = 8, bg = "white")

# Plot
mp <- gg_Manhattan_xModels(
  # Specify a folder with GWAS results
  folder = "GWAS_Results/",
  # Select traits to plot
  traits = c("DTF_Nepal_2017", "DTF_Sask_2017", "DTF_Sask_2017_b"),
  # Specify a title
  title = "Days to Flower",
  # Set horizontal thresholds bars
  threshold = 6.7,
  sug.threshold = 5,
  # Add vertical lines
  vlines = c("Lcu.1GRN.Chr2p44545877",
              "Lcu.1GRN.Chr5p1658484",
              "Lcu.1GRN.Chr6p3269280"),
  vline.colors = c("red", "red", "blue"),
  vline.types = c(2,2,1),
  # Change the legend alignment
  legend.box="vertical",
  # Choose a GWAS model
  models =  "MLM")
# Save
ggsave("figures/gg_Manhattan_xModels_03.png", mp, width = 12, height = 3.5, bg = "white")