View source: R/functions_for_RGWAS.R
manhattan | R Documentation |
Draw manhattan plot
manhattan(
input,
sig.level = 0.05,
method.thres = "BH",
y.max = NULL,
cex = 1,
cex.lab = 1,
lwd.thres = 1,
plot.col1 = c("dark blue", "cornflowerblue"),
cex.axis.x = 1,
cex.axis.y = 1,
plot.type = "p",
plot.pch = 16
)
input |
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. |
sig.level |
Significance level for the threshold. The default is 0.05. |
method.thres |
Method for detemining threshold of significance. "BH" and "Bonferroni are offered. |
y.max |
The maximum value for the vertical axis of manhattan plot. If NULL, automatically determined. |
cex |
A numerical value giving the amount by which plotting text and symbols should be magnified relative to the default. |
cex.lab |
The font size of the labels. |
lwd.thres |
The line width for the threshold. |
plot.col1 |
This argument determines the color of the manhattan plot. You should substitute this argument as color vector whose length is 2. plot.col1[1] for odd chromosomes and plot.col1[2] for even chromosomes. |
cex.axis.x |
The font size of the x axis. |
cex.axis.y |
The font size of the y axis. |
plot.type |
This argument determines the type of the manhattan plot. See the help page of "plot". |
plot.pch |
This argument determines the shape of the dot of the manhattan plot. See the help page of "plot". |
Draw manhttan plot
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