old_gg_Manhattan — old_gg_Manhattan • gwaspr

Creates a manhattan plot. Note: this function is meant for the old version of GAPIT.

Usage

old_gg_Manhattan(
  folder,
  trait,
  title = trait,
  threshold = NULL,
  sug.threshold = NULL,
  markers = NULL,
  labels = markers,
  vlines = markers,
  vline.colors = rep("red", length(vlines)),
  vline.legend = F,
  facet = T,
  qq = T,
  pmax = NULL,
  models = c("MLM", "MLMM", "FarmCPU", "Blink", "GLM"),
  chrom.colors = c("darkgreen", "darkgoldenrod3", "darkgreen", "darkgoldenrod3",
    "darkgreen", "darkgoldenrod3", "darkgreen"),
  model.colors = c("darkgreen", "darkred", "darkorange3", "steelblue", "darkorchid4",
    "darkgoldenrod2")
)

Arguments

folder: Folder containing GWAS results.
trait: The trait to read.
title: A title for the plot.
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.legend: Logical, wheterh or not to add a legend for the vlines.
facet: Logical, whether or not to produce a facetted or multi-model plot.
qq: Logical, whether or not to add a QQ plot
pmax: A max value for the y-axis.
models: Models to read.
chrom.colors: Colors for each chromosome. Used if `facet = T`.
model.colors: Colors for each model. Used if `facet = F`.

Value

A manhattan plot.