Manhattan plot
Draws a Manhattan plot
manhattan(x, bty = "n", chrom.col = c("black", "gray50"), thinning = TRUE, ... )x |
A data.frame with columns named |
bty |
Type of box to draw about the plot. Default is to draw none. |
thinning |
|
chrom.col |
Alternating colors for chromosomes. |
... |
Graphical parameters to be passed to |
If there is only one chromosome value in x$chr, the x-axis will be labeled with the SNP
position. In the general case, the x-axis is labeled with the chromosome name and the color
of the points alternates between the colors in chrom.col.
The default value bty = "n" should give the best result for GWAS Manhattan plots.
See par for other possible values of bty and their meaning.
The thinning procedure suppress some points to avoid generating too heavy graphs. The user
should check that setting thinning = FALSE does not change the final aspect of the
plot.
An invisible copy of x is returned, in which a column coord has been added
if there is more than one chromosome value in x$chr. This column contains the x-coordinates of each
SNP on the plot, and should prove helpful to annotate it.
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