gg_Manhattan_Traits — gg_Manhattan

Creates a manhattan plot.

Usage

gg_Manhattan_Traits(
  folder,
  traits,
  title = "GWAS",
  threshold = NULL,
  sug.threshold = NULL,
  vlines = markers,
  vline.colors = rep("red", length(vlines)),
  vline.types = rep(1, length(vlines)),
  vline.legend = F,
  markers = NULL,
  labels = markers,
  facet = F,
  addQQ = T,
  pmax = NULL,
  model = "MLM",
  myColors = c("darkgreen", "darkred", "darkorange3", "steelblue", "darkorchid4"),
  chrom.unit = "100 Mbp",
  legend.rows = 1
)

Arguments

folder: Folder containing GWAS results.
traits: The traits to read.
title: A title for the plot.
threshold: Significant Threshold.
sug.threshold: Suggested threshold.
vlines: Markers which will be used as a location for a vertical lines.
vline.colors: colors for each vertical line.
vline.types: lty for each vertical line.
vline.legend: Logical, whether or not to add a legend for the vlines.
markers: Markers to be labelled.
labels: Labels to be used for markers.
facet: Logical, whether or not to produce a facetted or multi-model plot.
addQQ: Logical, whether or not to add a QQ plot
pmax: A max value for the y-axis.
model: Model to read.
myColors: Colors for each trait.
chrom.unit: Unit for the x-axis. Can be one of c("kbp","100 kbp","Mbp","100 Mbp","Gbp").
legend.rows: Number of rows for the legend.

Value

A manhattan plot.