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Creates a manhattan plot.

Usage

gg_Manhattan(
  folder,
  trait,
  title = trait,
  threshold = NULL,
  sug.threshold = NULL,
  markers = NULL,
  labels = markers,
  vlines = markers,
  vline.color = "red",
  facet = T,
  qq = T,
  pmax = NULL,
  models = c("MLM", "MLMM", "FarmCPU", "Blink", "GLM"),
  colors1 = c("darkgreen", "darkgoldenrod3", "darkgreen", "darkgoldenrod3",
    "darkgreen", "darkgoldenrod3", "darkgreen"),
  colors2 = c("darkgreen", "darkred", "darkorange3", "steelblue", "darkorchid4",
    "darkgoldenrod2")
)

Arguments

folder

Folder containing GWAS results.

trait

The trait to read.

title

A title for the plot.

markers

Markers to be labelled.

labels

Labels to be used for markers.

vlines

Markers which will be used as a location for a vertical lines.

vline.color

color for each vertical line.

facet

Logical, whether or not to produce a facetted or multi-model plot.

qq

Logical, whether or not to add a QQ plot

pmax

A max value for the y-axis.

models

Models to read.

colors1

Colors for each chromosome.

colors2

Colors for each model.

Value

A manhattan plot.