plotManhattan: Create a Manhattan plot from rTASSEL association output

In maize-genetics/rTASSEL: R Front-End for TASSEL

Create a Manhattan plot from rTASSEL association output

Description

This function allows for quick generation of a Manhattan plot from rTASSEL association statistical output data.

Usage

plotManhattan(
  assocRes,
  trait = NULL,
  threshold = NULL,
  colors = c("#91baff", "#3e619b"),
  interactive = FALSE,
  pltTheme = c("default", "classic")
)

Arguments

assocRes	An object of type AssociationResults
trait	Which phenotypic trait do you want to plot? If set to NULL, this will generate a faceted plot with all mapped traits
threshold	User-defined -log_{10}(p)-value threshold for significant marker determination. Once specified any marker points higher than this line will be highlighted.
colors	A vector of character colors used for differentiating multiple chromosomes. Defaults to 2 shades of blue.
interactive	Do you want to produce an interactive visualization? Defaults to FALSE.
pltTheme	What theme would like to display for the plot? Only supports one theme currently.

Value

Returns a ggplot2 object

maize-genetics/rTASSEL documentation built on Nov. 13, 2023, 7:18 a.m.