Question: different color for highlighting genes in Manhattan plot in qqman
1
gravatar for Line Heylen
4.0 years ago by
Line Heylen20
Belgium
Line Heylen20 wrote:

Hi,

I'm using qqman in R to draw a Manhattan plot (not SNPs, but DNA methylation data of 450K Illumina arrays, but this won't make a difference for this particular question). 

I can highlight specific CpGs of interest using the highlight = in the manhattan function, however, I would like to change this color green to a different more visible color (like red). I do not find any information on whether I can change this highlight color, only on how to change the colors per chromosome. 

This is the code I use: 

qqman::manhattan(a, chr = "CHR", bp = "MAPINFO", p = "P.value", snp = "CPG.Labels", main = "Manhattan Plot", chrlabs = c(1:22), suggestiveline = -log10(1e-05), cex = 0.6, cex.axis = 0.9, genomewideline = -log10(5e-08), highlight = b, logp = TRUE)

I'm not a bio-informaticican, but need to use R for my analyses, so please excuse me if this is a very obvious question.

Thank you very much for your help and time.

Kind regards,

Line

R genome • 3.5k views
ADD COMMENTlink written 4.0 years ago by Line Heylen20

Hi. Did you ever get an answer? I find the green color to be pretty ugly!

ADD REPLYlink written 15 months ago by lakemonster0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1989 users visited in the last hour