Change the color

[chenglishen2018]

I tried to revise the color in the Manhattan plot, but not successful. By default, the colors are repeated, such as genomes 1,9 and 17 are the same color. Can I revise the default color?

[swannyy14]

Hi @chenglishen2018 , guide to customizing point color with ggmanh package can be found in this link.

If you wish to color the points based on chromosome using manhattan_plot() function, you can pass the column name to the argument highlight.colname= and pass a character vector to the argument highlight.col=.

For example, if you have a dataset data with chromosome as column name, which contains chromosome 1, 2, and X, then specifying manual color would look something like

manh_colormap <- c("1" = "red", "2" = "green", "X" = "blue")
manhattan_plot(data = data, ---other necessary arguments---, highlight.colname = "chromosome", highlight.col = manh_colormap)