How to plot positions along a chromosome graphic

Question

I would like to generate a plot depicting 14 linear chromosomes for the organism I work on, to scale, with coloured bars at specified locations along each chromosome. Ideally I\

Answer 1

Just save your barplot call and then call segments to make the marks at an appropriate location. E.g.:

bp <- barplot(dat$size, border=NA, col="grey80")

with(marks,
  segments(
    bp[Chromosome,]-0.5,
    Position,
    bp[Chromosome,]+0.5,
    Position,
    col=Type,
    lwd=2, 
    lend=1
   )
)

Data used:

dat <- structure(list(chromosome = 1:14, size = c(640851L, 947102L, 
1067971L, 1200490L, 1343557L, 1418242L, 1445207L, 1472805L, 1541735L, 
1687656L, 2038340L, 2271494L, 2925236L, 3291936L)), .Names = c("chromosome", 
"size"), class = "data.frame", row.names = c(NA, -14L))

marks <- structure(list(Chromosome = c(3L, 12L, 13L, 5L, 11L, 14L), Position = c(817702L, 
1556936L, 1131566L, 1041685L, 488717L, 1776463L), Type = structure(c(1L, 
1L, 1L, 2L, 2L, 2L), .Label = c("A", "B"), class = "factor")), .Names = c("Chromosome", 
"Position", "Type"), class = "data.frame", row.names = c(NA, 
-6L))