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Creates a manhattan plot comparing the NYC and Kansas results.

Usage

gg_NYCvsKansas(
  folder = "GWAS_Results/",
  trait = list_Traits(folder)[1],
  title = trait,
  threshold = NULL,
  sug.threshold = NULL,
  chrom = NULL,
  markers = NULL,
  labels = markers,
  vlines = markers,
  vline.colors = rep("red", length(vlines)),
  vline.types = rep(1, length(vlines)),
  vline.legend = T,
  addQQ = T,
  pmax = NULL,
  models = c("FarmCPU", "BLINK"),
  sig.col = "darkred",
  chrom.colors = rep(c("darkgreen", "darkgoldenrod3"), 30),
  chrom.unit = "100 Mbp",
  legend.rows = 1,
  plotHBPvalues = F
)

Arguments

folder

Folder containing GWAS results.

trait

The trait to read.

title

A title for the plot.

threshold

Significant Threshold.

sug.threshold

Suggested threshold.

chrom

Chromosomes to plot. Use if you want to plot a single chromosome.

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.

addQQ

Logical, whether or not to add a QQ plot

pmax

A max value for the y-axis.

models

Models to read.

sig.col

Color for significant assoctiations. Used if `facet = T`.

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.

plotHBPvalues

Logical, if TRUE, H.B.P.Values be uses.

Value

A manhattan plot.