gg_GWAS_Summary

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),
  threshold = round(-log10(5e-08), 1),
  sug.threshold = round(-log10(5e-06), 1),
  chroms = NULL,
  pos1 = NULL,
  pos2 = NULL,
  models = c("MLM", "FarmCPU", "BLINK", "MLMM", "GLM", "CMLM", "SUPER"),
  colors = c("darkgreen", "darkorange3", "steelblue", "darkred", "darkorchid4",
    "burlywood4", "darkseagreen4"),
  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 = NULL
)

Arguments

folder

Folder containing GWAS results.

traits

The traits to read.

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.

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.