mash_plot_manhattan_by_condition: Manhattan plot in ggplot colored by significant conditions

In Alice-MacQueen/switchgrassGWAS: Genome Wide Association on Panicum virgatum

Description

Takes a mash object and, for some vector of phenotypes, returns a Manhattan plot ggplot object (and its dataframe). Each SNP in the plot is colored by the number of phenotypes it is significant for. Even and odd chromosomes have different shapes for their SNPs, so that chromosome identity can be determined.

Usage

mash_plot_manhattan_by_condition(
  m,
  cond = NA,
  saveoutput = FALSE,
  suffix = "",
  thresh = 0.05
)

Arguments

m	A mash object (outputted by mash).
cond	A vector of phenotypes. Defaults to the names of each column in the mash object.
saveoutput	Logical. Should the output be saved to the path?
suffix	Character. Optional. A unique suffix used to save the files, instead of the current date & time.
thresh	Numeric. The threshold used for the local false sign rate to call significance in a condition.

Value

A tbl_df() of the data used to make the Manhattan plot, and a ggplot object containing the Manhattan.

Examples

## Not run: manhattan_out <- mash_ggman_by_condition(m = m, saveoutput = TRUE)

Alice-MacQueen/switchgrassGWAS documentation built on Jan. 23, 2022, 7:55 p.m.