gg_GWAS_Summary — gg_GWAS_Summary • gwaspr

Creates a summary GWAS plot of significant associations. Note: this function requires the GWAS results files to be ordered

Usage

gg_GWAS_Summary(
  folder = "GWAS_Results/",
  traits = list_Traits(folder),
  groups = NULL,
  threshold = round(-log10(5e-08), 1),
  sug.threshold = round(-log10(5e-06), 1),
  chroms = NULL,
  pos1 = NULL,
  pos2 = NULL,
  models = c("MLM", "MLMM", "FarmCPU", "BLINK", "GLM", "CMLM", "SUPER"),
  model.colors = gwaspr_Colors,
  shapes = 21:25,
  hlines = NULL,
  vlines = NULL,
  vline.colors = rep("red", length(vlines)),
  vline.types = rep(1, length(vlines)),
  vline.legend = T,
  title = "Summary of Significant GWAS Results",
  caption = paste0("Significant Threshold = ", threshold,
    " = Large\nSuggestive Threshold = ", sug.threshold, " = Small"),
  rowread = 2000,
  legend.position = "bottom",
  legend.rows = 1,
  plotHBPvalues = F,
  skyline = "Kansas"
)

Arguments

folder: Folder containing GWAS results.
traits: The traits to read.
groups: Grouping for the traits. Should be equal length to `traits`.
threshold: Significant threshold.
sug.threshold: Suggestive threshold.
chroms: Chromosomes to plot.
pos1: starting position to plot.
pos2: ending position to plot.
models: Models to read.
model.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.
plotHBPvalues: Logical, should H.B.P.Values be uses.
skyline: Which skyline type to use. Can be "NYC" or "Kansas". If left NULL, it will use the highest P.value.

Value

A GWAS summary plot.