2023/03/27 2:49

There are several R packages available for making Manhattan plots for GWAS data. One popular package is “qqman”. Here’s an example code using “qqman” package:

Library(qqman)

data <- read.table(" your GWAS data.txt", header = T)

manhattan(data, col = c(“blue4″, “orange3”), cex=0.8

In the code above, replace “your_GWAS_data.txt” with the name of your GWAS data file. The ~col* argument specifies the color of the points in the plot and ~cex* argument adjusts the size of the points. You can adjust these arguments to customize the appearance of the plot.

Note that the input data for ~manhattanQ~ function should contain at least two columns: the first column for chromosome numbers and the second column for -log10 transformed p-values (or another statistic of interest).