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Creates a manhattan plot.

Usage

gg_Manhattan(
  folder,
  trait,
  title = trait,
  threshold = NULL,
  sug.threshold = NULL,
  vlines = markers,
  vline.colors = rep("red", length(vlines)),
  vline.legend = F,
  markers = NULL,
  labels = markers,
  facet = F,
  addQQ = T,
  pmax = NULL,
  models = c("MLM", "MLMM", "FarmCPU", "BLINK", "GLM"),
  model.colors = c("darkgreen", "darkred", "darkorange3", "steelblue", "darkorchid4"),
  chrom.colors = rep(c("darkgreen", "darkgoldenrod3"), 30),
  chrom.unit = "100 Mbp",
  legend.rows = 2
)

Arguments

folder

Folder containing GWAS results.

trait

The trait 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.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.

models

Models to read.

model.colors

Colors for each model. Used if `facet = F`.

chrom.colors

Colors for each chromosome. Used if `facet = T`.

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.