Creates a manhattan plot.
snp_manhattan(gwas, infos.chr, infos.pos, colors = c("black", "grey60"), dist.sep.chrs = 1e+07, ind.highlight = integer(0), col.highlight = "red", labels = NULL, npoints = NULL, coeff = 1)
Vector of integers specifying each SNP's chromosome.
Vector of integers specifying the physical position
on a chromosome (in base pairs) of each SNP.
Colors used for each chromosome (they are recycled). Default is an alternation of black and gray.
"Physical" distance that separates two chromosomes. Default is 10 Mbp.
Indices of SNPs you want to highlight (of interest). Default doesn't highlight any SNPs.
Color used for highlighting SNPs. Default uses red.
Labels of the x axis. Default uses the number of the
chromosome there are in
Number of points to keep (ranked by p-value) in order to get
a lighter object (and plot). Default doesn't cut anything.
If used, the resulting object will have an attribute called
Relative size of text. Default is
ggplot2 object. You can plot it using the
If you don't have information of chromosome and position, you should simply
set.seed(9) test <- snp_attachExtdata() G <- test$genotypes y <- rnorm(nrow(G)) gwas <- big_univLinReg(G, y) snp_qq(gwas)# The next plot should be prettier with a real dataset snp_manhattan(gwas_gc, infos.chr = test$map$chromosome, infos.pos = test$map$physical.pos)