gg_Manhattan_Zoom — gg_Manhattan

Creates a manhattan plot zoomed in to a particular region.

Usage

gg_Manhattan_Zoom(
  folder = "GWAS_Results/",
  trait = list_Traits(folder)[1],
  chrom,
  pos1,
  pos2,
  title = trait,
  threshold = NULL,
  sug.threshold = NULL,
  markers = NULL,
  labels = markers,
  vlines = markers,
  vline.colors = "red",
  sig.col = "red",
  models = c("MLM", "FarmCPU", "BLINK", "MLMM", "GLM", "CMLM", "SUPER"),
  model.colors = c("darkgreen", "darkorange3", "steelblue", "darkred", "darkorchid4",
    "burlywood4", "darkseagreen4"),
  facet = F,
  highlight.sig = F,
  highlight.marker.color = "red",
  legend.rows = 1,
  plotHBPvalues = F,
  skyline = NULL
)

Arguments

folder: Folder containing GWAS results.
trait: The trait to read.
chrom: Chromosome to plot.
pos1: Start position on chromosome.
pos2: End position on chromosome.
title: A title for the plot.
threshold: Significant Threshold.
sug.threshold: Suggested threshold.
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.colors: colors for each vertical line.
sig.col: Color for significant assoctiations.
models: Models to read.
facet: Logical, whether or not to produce a facetted or multi-model plot. Default is `facet = F`.
highlight.sig: Logical, whether or not to highlight significant associations with a black circle. Used if `facet = F`.
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 manhattan plot.