gg_GWAS_Summary — gg_GWAS_Summary • gwaspr

Creates a summary GWAS plot of significant associations.

Usage

gg_GWAS_Summary(
  folder = NULL,
  traits = list_Traits(),
  threshold = -log10(5e-08),
  sug.threshold = -log10(5e-06),
  models = c("MLM", "MLMM", "FarmCPU", "BLINK", "GLM"),
  colors = c("darkgreen", "darkred", "darkorange3", "steelblue", "darkgoldenrod2"),
  shapes = 21:25,
  hlines = NULL,
  vlines = NULL,
  vline.colors = rep("red", length(vlines)),
  vline.types = rep(1, length(vlines)),
  vline.legend = T,
  title = NULL,
  caption = paste0("Sig Threshold = ", threshold, " = Large\nSuggestive = ",
    sug.threshold, " = Small"),
  rowread = 2000,
  legend.position = "bottom",
  legend.rows = 1
)

Arguments

folder: Folder containing GWAS results.
traits: The traits to read.
threshold: Significant threshold.
sug.threshold: Suggestive threshold.
models: Models to read.
colors: Colors for each model.
shapes: The shape values to use for the different models. e.g., 21:25
hlines: Locations for horizontal lines. e.g., hlines = c(1.5,2.5).
vlines: Markers to be labelled with a vertical red line.
vline.colors: colors for each vertical line.
vline.types: lty for each vertical line.
vline.legend: Logical, display of vline color legend.
title: A title for the plot.
caption: A caption for the plot.
rowread: Number of rows to read for each GWAS results file.
legend.rows: Number of rows for the legend.

Value

A GWAS summary plot.