plotpos.by.chr: Utilities for Manhatten plots
In tobyjohnson/gtx: Genetics ToolboX

Description Usage Arguments Details Value Author(s) Examples

Constructs vectors of plotting positions and colours, for points that have positions on chromosomes.

plotpos.by.chr(chr, pos, gap = 5e7,
               chrset = c(1:22, "XY", "X", "Y", "M"))
plotcol.by.chr(chr, cols = NULL, col.missing = "black",
               chrset = c(1:22, "XY", "X", "Y", "M"))
axis.by.chr(chr, plotpos, side = 1, lines = 2)

`chr`	A vector of chromosome identities
`pos`	A vector of positions within chromosomes
`gap`	Gap size between chromosomes, in same units as `pos`
`chrset`	Set of all chromosomes
`cols`	Colours for chromosomes, recycled as necessary
`col.missing`	Colour to use for chromosomes not in `chrset`
`plotpos`	A vector of plotting positions
`side`	Side to plot the axis
`lines`	Number of lines to distribute chromosome labels over

These functions all convert chr to upper case and remove leading “CHR” if present, before doing anything else.

If argument cols to plotcol.by.chr is left NULL, it is filled with a suitable call to contrasting.rainbow. For an alternative popular style of Manhatten plot, try cols = c("cyan", "grey").

The example illustrates how to use these functions to help draw a Manhatten plot.

plotpos.by.chr returns a vector of plotting positions of length equal to the input chr and pos.

plotcol.by.chr returns a vector of plotting colours of length equal to the input chr.

axis.by.chr draws an axis and returns the positions the ticks were drawn at.

Toby Johnson Toby.x.Johnson@gsk.com

## generate dummy GWAS results
gwas <- data.frame(chr = paste("chr", rep(1:22, each = 500), sep = ""),
                   pos = do.call(c, lapply(1:22, function(chr)
return(sort(ceiling(runif(500, 1, 1e8/chr)))))),
                   pval = runif(11000),
                   stringsAsFactors = FALSE)
## example drawing a Manhatten plot
gwas$plotpos <- plotpos.by.chr(gwas$chr, gwas$pos)
gwas$plotcol <- plotcol.by.chr(gwas$chr)
with(gwas, plot(plotpos, -log10(pval), col = plotcol,
                ann = FALSE, xaxt = "n", las = 1))
title(ylab = expression(-log[10](italic(P))))
axis.by.chr(gwas$chr, gwas$plotpos)
mtext("Genomic position by chromosome", side = 1, line = 3)