gg_Manhattan — gg_Manhattan • gwaspr

Create manhattan plots from GAPIT GWAS results.

Usage

gg_Manhattan(
  folder = "GWAS_Results/",
  trait = list_Traits(folder)[1],
  title = trait,
  threshold = NULL,
  sug.threshold = NULL,
  chr = NULL,
  markers = NULL,
  labels = markers,
  vlines = markers,
  vline.colors = rep("red", length(vlines)),
  vline.types = rep(1, length(vlines)),
  legend = T,
  legend.rows = 1,
  legend.box = "horizontal",
  point.sizes = c(0.3, 1, 0.75),
  pmax = NULL,
  pmin = 0,
  models = c("MLM", "MLMM", "FarmCPU", "BLINK", "GLM", "CMLM", "SUPER"),
  model.colors = c("darkgreen", "darkred", "darkorange3", "steelblue", "darkorchid4",
    "blue2", "magenta3"),
  facet = F,
  highlight.sig = F,
  sig.color = "black",
  chr.colors = rep(c("darkgreen", "darkgoldenrod3"), 30),
  chr.unit = "100 Mbp",
  plotHBPvalues = F,
  skyline = NULL,
  addQQ = T
)

Arguments

folder: Folder containing GWAS results.
trait: The trait to read.
title: A title for the plot.
threshold: Significant Threshold.
sug.threshold: Suggested threshold.
chr: 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.
legend: Logical, whether or not to add a legend.
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").
pmax: A max value for the y-axis. Markers with higher values will be lowered to pmax..
pmin: A min Value for plotting. Markers with lower values will be removed.
models: Models to read.
model.colors: Colors for each model. Used if facet = F.
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.
sig.color: Color for significant assoctiations. Used if facet = T.
chr.colors: Colors for each chromosome. Used if facet = T.
chr.unit: Unit for the x-axis. Can be one of c("kbp","100 kbp","Mbp","100 Mbp","Gbp").
plotHBPvalues: Logical, if TRUE, H.B.P.values be uses.
skyline: Which skyline type to use. Can be "NYC" or "Kansas". If NULL, it will use the highest P.value.
addQQ: Logical, whether or not to add a QQ plot.

Value

A manhattan plot.