gg_Manhattan_Zoom_Traits — gg_Manhattan_Zoom

Create manhattan plots for multiple traits zoomed in to a particular region.

Usage

gg_Manhattan_Zoom_Traits(
  folder = "GWAS_Results/",
  traits = list_Traits(folder)[1],
  title = NULL,
  chr,
  pos1 = NULL,
  pos2 = NULL,
  threshold = NULL,
  sug.threshold = NULL,
  markers = NULL,
  labels = markers,
  vlines = markers,
  vline.colors = rep("red", length(vlines)),
  vline.types = rep(1, length(vlines)),
  vline.legend = T,
  pmax = NULL,
  models = c("MLM", "MLMM", "FarmCPU", "BLINK", "GLM", "CMLM", "SUPER"),
  model.colors = c("darkgreen", "darkred", "darkorange3", "steelblue", "darkorchid4",
    "blue2", "magenta3"),
  sig.color = "black",
  legend.rows = 1,
  legend.box = "horizontal",
  point.sizes = c(0.3, 1, 0.75),
  plotHBPvalues = F,
  skyline = NULL
)

Arguments

folder: Folder containing GWAS results.
traits: The traits to read.
title: A title for the plot.
chr: Chromosome to plot.
pos1: Start position on chromosome.
pos2: End position on chromosome.
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.
vline.types: lty for each vertical line.
vline.legend: Logical, whether or not to add a legend for the vlines.
pmax: A max value for the y-axis.
models: Models to read.
model.colors: Colors for each model.
sig.color: Color for significant assoctiations.
legend.rows: Number of rows for the legend.
legend.box: Alignment of the legend. Default is "horizontal", but it can be changed to "vertical".
point.sizes: Sizes for the points. c("Not Sig", "Sig", "Sug").
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.