ggman: Creates a Manhattan Plot.
In drveera/ggman: R package for Manhattan Plots

Description Usage Arguments Details Value Examples

Creates a Manhattan Plot as a ggplot layer.

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, ...)

`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

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.

A Manhattan Plot

#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")