manhattanPlot: Create Manhattan plot from rTASSEL association output

In maize-genetics/bioconductor_test: R front-end for TASSEL

Description

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

Usage

manhattanPlot(assocStats, trait, threshold, colors = c("#91baff",
  "#3e619b"), showSigMarkers = FALSE)

Arguments

assocStats	rTASSEL association statistical output. This output is derived from association output dat frames ending in _Stats. This data contains the necessary column variables for this plot to work.
trait	Which phenotypic trait do you want to plot?
threshold	User-defined p-value threshold for significant marker determination. Once specified any marker points higher than this line will be highlighted.
colors	A vector of colors used for differentiating multiple chromosomes. Defaults to 2 shades of blue.
showSigMarkers	Should significantly highlighted markers be labelled? If TRUE, marker points will labelled with their respective marker labels. Defaults to FALSE.

Value

Returns a ggplot2 object

maize-genetics/bioconductor_test documentation built on Nov. 4, 2019, 5:19 p.m.