ggman: Creates a Manhattan Plot.

In veera-dr/ggman: R package for Manhattan Plots

Description

Creates a Manhattan Plot as a ggplot layer.

Usage

ggman(gwas, clumps = NA, snp = NA, bp = NA, chrom = NA, pvalue = NA,
  sigLine = 8, lineColour = "red", pointSize = 0.1, ymin = NA,
  ymax = NA, logTransform = TRUE, invert = FALSE, invert.method = "or",
  invert.var = "or", relative.positions = FALSE, xlabel = "chromosome",
  ylabel = "-log10(P value)", title = "Manhattan Plot",
  legend.title = "legend", clumps.label.type = "label",
  legend.remove = FALSE, ...)

Arguments

gwas	A data frame with the gwas results
clumps	Optional argument; takes an object of class 'ggclumps' containing the SNP clumps, see ggmanClumps
snp	Name of the column containing SNP identifiers; default is 'snp'
bp	Name of the column containing the basepair positions; default is 'bp'
chrom	Name of the column containing the chromosome identifers; default is 'chrom'
pvalue	Name of the column containing the p values; default is 'pvalue'
sigLine	Threshold for the genome wide significant line in -log10 scale; default is 8; specify NA to remove the line.
lineColour	colour of the genomewide line; default is 'red'
pointSize	Size of the points in the plot; default is 0.1
ymin	Starting point of y axis; default is 0
ymax	Ending point of y axis
logTransform	if TRUE, P value is -log10 transformed; default is TRUE; Specify FALSE when plotting values other p values, such as zscore or beta
invert	if TRUE, an inverted Manhattan Plot will be created. The p values of the variants with (or < 1 or beta < 0) will positive log10-transformed, which will result in negative values.
invert.method	whether inversion should be based on odds ratio or beta. possible values: 'or' or 'beta'
invert.var	name of the column in the gwas data.frame containing the or or beta
relative.positions	if TRUE, the x axis points will be calculated in proportion to the basepair positions. So, the gaps in the genome with no genotypes will be reflected in the plot(requires more computation, hence more time to plot). If FALSE, the SNPs are ascendingly sorted chromosome-wise. The default value is FALSE.
xlabel	X-axis label
ylabel	Y-axis label
title	plot title
legend.title	title of legend; this argument applies only when the clumps are plotted and highlighted in groups.
clumps.label.type	type of label; either 'text' or 'label'; default is 'label'
legend.remove	if TRUE, the legend will be removed; default is FALSE
...	other arguments to pass to geom_point; Note: do not use size to specify size of the points, instead use pointSize

Details

The function creates a manhattan plot as a ggplot layer. The output can be stored in a variable, and additional layers can be added. See ggmanHighlight, ggmanZoom and ggmanLabel.

Value

A Manhattan Plot

Examples

#simple Manhattan Plot
ggman(toy.gwas, snp = "snp", bp = "bp", chrom = "chrom",
pvalue = "pvalue")

#enable relative positioning
ggman(toy.gwas, snp = "snp", bp = "bp", chrom = "chrom",
pvalue = "pvalue",relative.positions = TRUE)

#plot odds ratio
ggman(toy.gwas, snp = "snp", bp = "bp", chrom = "chrom",
pvalue = "or",logTransform = FALSE, ymax = 3)

#plot beta
ggman(toy.gwas, snp = "snp", bp = "bp", chrom = "chrom", pvalue = "beta",
logTransform = FALSE, ymin = -2, ymax = 2)

#inverted Manhattan plot 
ggman(toy.gwas, snp = "snp", bp = "bp", chrom = "chrom", pvalue = "pvalue",
invert = TRUE, invert.method = 'or', invert.var = "or")

veera-dr/ggman documentation built on May 3, 2019, 4:59 p.m.