posts/plotting_ethnic_regions.mdwn

   1 [[!meta title="Plotting Ethnic Regions"]]
   2
   3 I was asked over the weekend how to plot SNPs which are associated
   4 with specific ethnicities; the following code is a really quick stab
   5 at the problem using the grid graphics engine in R.
   6
   7 [[!sweavealike fig=1 echo=1 results="hide" code="""
   8 require(grid)
   9 snp.position <- 1:10
  10 snp.integers <- sample.int(5,size=length(snp.position),replace=TRUE)
  11 ### the position is really the midpoint of the range
  12 snp.midpoint <- snp.position
  13 ### start of the SNP; we're assuming it should start at 0.
  14 snp.start <- c(0,snp.position[-1]-diff(snp.position)/2)
  15 ### stop of the snp; we're assuming it should stop at the last snp position
  16 snp.stop <- c(snp.position[-length(snp.position)]+diff(snp.position)/2,
  17         snp.position[length(snp.position)])
  18 snp.width <- snp.stop - snp.start
  19
  20 ### these are the colors
  21 possible.colors <- c("red","blue","yellow","green","purple")
  22 snp.colors <- possible.colors[snp.integers]
  23
  24 ### this sets up the viewport that we'll plot into
  25 pushViewport(viewport(height=unit(1,"npc")-unit(7,"lines"),
  26 width=unit(1,"npc")-unit(7,"lines")
  27         ))
  28 pushViewport(dataViewport(xscale=range(c(0,snp.stop)),yscale=c(0,1)))
  29
  30 ### this draws a rectangle around the graph
  31 grid.rect()
  32 ### this sets up the x axis
  33 grid.xaxis()
  34 ### this labels the X axis
  35 grid.text("Position on Chromosome",y=unit(-2.5,"lines"))
  36
  37 ### this draws all of the boxes corresponding to each SNP in the
  38 ### appropriate color
  39 grid.rect(x=unit(snp.start,"native"),
  40         width=unit(snp.width,"native"),
  41         y=unit(0.5,"native"),
  42         height=unit(0.25,"native"),just=c("left","center"),
  43         gp=gpar(col=snp.colors,fill=snp.colors))
  44
  45 ### this pops the viewport
  46 popViewport(2)
  47 """]]
  48
  49
  50 [[!tag r genetics biology]]