% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/mash-evaluation.R
\name{mash_plot_manhattan_by_condition}
\alias{mash_plot_manhattan_by_condition}
\title{Manhattan plot in ggplot colored by significant conditions}
\usage{
mash_plot_manhattan_by_condition(
  m,
  snp,
  cond = NA,
  saveoutput = FALSE,
  suffix = "",
  thresh = 0.05
)
}
\arguments{
\item{m}{A mash object (outputted by mash).}

\item{snp}{A bigSNP object, produced by the bigsnpr package. Here,
the WAMI SNP information.}

\item{cond}{A vector of phenotypes. Defaults to the names of each
column in the mash object.}

\item{saveoutput}{Logical. Should the output be saved to the path?}

\item{suffix}{Character. Optional. A unique suffix used to save the files,
instead of the current date & time.}

\item{thresh}{Numeric. The threshold used for the local false sign rate to
call significance in a condition.}
}
\value{
A \code{tbl_df()} of the data used to make the Manhattan plot, and a
ggplot object containing the Manhattan.
}
\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.
}
\examples{
\dontrun{manhattan_out <- mash_ggman_by_condition(m = m, saveoutput = TRUE)}

}