man_plot: Manhattan Plot

In gwaRs: Manhattan, Q-Q, and PCA Plots using 'ggplot2'

Description

Creates a Manhattan plot

Usage

man_plot(
  data,
  chromCol = c("gray44", "black"),
  genomewideline = -log10(5e-08),
  suggestiveline = -log10(1e-05),
  chromosome = "ALL",
  annotatePval = FALSE,
  annotateSNP = NULL,
  annotateCol = "red",
  highlight = NULL,
  highlightCol = "green3",
  title = NULL
)

Arguments

data	PLINK assoc output, tab-delimited, or a data.frame with "SNP", "CHR", "BP", and "P" columns.
chromCol	A character vector indicating which colors to alternate for the chromosomes.
genomewideline	Where to draw the "genome-wide significant" line. Default -log10(5e-8). Set to FALSE or F to disable
suggestiveline	Where to draw the "suggestive" line. Default -log10(1e-5). Set to FALSE or F to disable.
chromosome	An integer indicating which chromosome to plot. Default is "ALL".
annotatePval	If set, SNPs with p-value less than or equal to this p-value will be annotated on the plot.
annotateSNP	A character vector of SNPs in your dataset to annotate. If some of the SNPs are not in your dataset, gwaRs will throw a warning message.
annotateCol	A string denoting the color to use for the annotations.
highlight	A character vector of SNPs in the dataset to highlight. If some of the SNPs are not in your dataset, gwaRs will throw a warning message. Default is NULL.
highlightCol	A string denoting the color to use to highlight the SNPs.
title	A string denoting the title to use for the plot. Default is 'Manhattan Plot'

Details

Creates a Manhattan plot from PLINK assoc output (or any tab-delimited file or data frame with "SNP", "CHR", "BP", and "P" columns).

Value

A Manhattan plot.

Author(s)

Lindokuhle Nkambule

Examples

man_plot(gwasData)

gwaRs documentation built on April 20, 2021, 1:07 a.m.