gg_Marker_Box — gg_Marker

Creates a marker plot with myG and myY objects.

Usage

gg_Marker_Box(
  xG,
  xY,
  traits,
  markers,
  marker.colors = gwaspr_Colors,
  remove.hets = T,
  plot.violin = T,
  plot.box = T,
  plot.points = T,
  box.width = 0.1,
  point.size = 1,
  point.beeswarm = F,
  myncol = NULL,
  title = NULL,
  legend.rows = 1,
  subtitle = paste(markers, collapse = "\n"),
  yLab = traits,
  cv.source = "xG",
  cv.name = NULL,
  cv.colors = NULL,
  cv.label = NULL
)

Arguments

xG: GWAS genotype object. Note: needs to be in hapmap format.
xY: GWAS phenotype object.
traits: Traits to plot.
markers: Markers to plot.
marker.colors: Colors to fill in the violin and boxplots.
remove.hets: Logical, Whether to remove hets or not. advisded if plotting multiple markers.
plot.violin: Logical, whether or not to plot violins.
plot.box: Logical, whether or not to plot the boxplots.
plot.points: Logical, whether or not to plot points.
box.width: Width for the boxplot.
point.size: Size for the points.
point.beeswarm: Logical. If False (the default), will plot points with geom_quasirandom. If TRUE, will plot points with geom_beeswarm.
myncol: Number of columns for facetting when plotting multiple traits.
title: Title for the plot.
legend.rows: Number of rows for the legend.
subtitle: Subtitle for the plot. Defaults to the list of markers.
yLab: Label for the y-axis.
cv.source: Where to get your cv.name from. Default is "xG", while "xY" is the other option.
cv.name: Covariable data for points.
cv.colors: Covariable colors for filling points.
cv.label: Label for the covariate.

Value

Marker plot.