Draw manhattan plot (another method)
manhattan2(
input,
sig.level = 0.05,
method.thres = "BH",
cex = 1,
plot.col2 = 1,
plot.type = "p",
plot.pch = 16,
cum.pos = NULL,
lwd.thres = 1,
cex.lab = 1,
cex.axis = 1
)Draw manhttan plot
Data frame of GWAS results where the first column is the marker names, the second and third column is the chromosome amd map position, and the forth column is -log10(p) for each marker.
Siginifincance level for the threshold. The default is 0.05.
Method for detemining threshold of significance. "BH" and "Bonferroni are offered.
A numerical value giving the amount by which plotting text and symbols should be magnified relative to the default.
Color of the manhattan plot. color changes with chromosome and it starts from plot.col2 + 1 (so plot.col2 = 1 means color starts from red.)
This argument determines the type of the manhattan plot. See the help page of "plot".
This argument determines the shape of the dot of the manhattan plot. See the help page of "plot".
Cumulative position (over chromosomes) of each marker
The line width for the threshold.
The font size of the labels.
The font size of the axes.