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gg_GWAS_Hits

gg_GWAS_Hits.Rd

Creates a summary GWAS plot of significant associations.

Usage

gg_GWAS_Hits(
  xx,
  xG,
  myTs,
  myR = 2e+06,
  myTitle = "",
  sigMin = 0,
  myCV = NULL,
  models = c("MLM", "MLMM", "FarmCPU", "BLINK", "GLM"),
  model.colors = c("darkgreen", "darkred", "darkorange3", "steelblue", "darkorchid4"),
  model.shapes = c(21, 24:25, 22, 23),
  vlines = NULL,
  vline.colors = rep("red", length(vlines)),
  vline.types = rep(1, length(vlines)),
  legend.rows = 1
)

Arguments

xx

Table of significant GWAS results. See ?table_GWAS_Results().

xG

Genotype data.

myTs

List of traits to use.

myR

Range for binning GWAS hits.

myTitle

Title for horizontal facet.

sigMin

Minimum number of hits to plot.

myCV

(optional) for filtering if you have a "CV" column.

models

Models to read.

model.colors

Colors for each model.

vlines

Markers to be labelled with a vertical red line.

vline.colors

colors for each vertical line.

vline.types

lty for each vertical line.

legend.rows

Number of rows for the legend.

Value

A GWAS Hits plot.