manhattan: Manhattan plot

In gaston: Genetic Data Handling (QC, GRM, LD, PCA) & Linear Mixed Models

Manhattan plot

Description

Draws a Manhattan plot

Usage

 manhattan(x, bty = "n", chrom.col = c("black", "gray50"), thinning = TRUE, ... ) 

Arguments

x	A data.frame with columns named chr, pos and p.
bty	Type of box to draw about the plot. Default is to draw none.
thinning	Logical. If TRUE, not all points are displayed.
chrom.col	Alternating colors for chromosomes.
...	Graphical parameters to be passed to plot.

Details

If there is only one chromosome value in x$chr, the x-axis will be labeled with the SNP position. In the general case, the x-axis is labeled with the chromosome name and the color of the points alternates between the colors in chrom.col.

The default value bty = "n" should give the best result for GWAS Manhattan plots. See par for other possible values of bty and their meaning.

The thinning procedure suppress some points to avoid generating too heavy graphs. The user should check that setting thinning = FALSE does not change the final aspect of the plot.

Value

An invisible copy of x is returned, in which a column coord has been added if there is more than one chromosome value in x$chr. This column contains the x-coordinates of each SNP on the plot, and should prove helpful to annotate it.

See Also

association.test, qqplot.pvalues, par, plot.default, points.default

gaston documentation built on May 29, 2024, 7:33 a.m.