Question

Here is my data and plot

nmar <- seq (1, 100, 5)
position= rep(nmar, 5)
n = length (nmar )
chr = rep(1:5, each = n )

mapdata <- data.frame (chr, position, 
 snpname = paste("SNP-", 1:length (position), sep = ""))
mapdata


chr.lab = 1 ; mbar.col = "blue"
layout(matrix(c(1,1,2),nc=1)) # works for two but I need to extend it to 
       n (which is level of chr = 5)

# plot level 1
mapdata1 <- mapdata[mapdata$chr == 1,]
m <- par()$mar
m[1] <- m[3] <- 0
par(mar=m)
# Set the limits of the  plot
plot(mapdata1$position,mapdata1$position-mapdata1$position, type="n",
   axes=FALSE, 
xlab="", ylab="Chromsome", yaxt="n" )

polygon(
  c(0,max(mapdata1$position + 0.08 * max(mapdata1$position)),max(mapdata1$position)+
     0.08 * max(mapdata1$position),0),
  .2*c(-0.3,-0.3,0.3,0.3),
  col= mbar.col
)
segments(mapdata1$position, -.3, mapdata1$position, .3 )
text(mapdata1$position, -.7, mapdata1$snpname, srt = 90, cex.lab = chr.lab)
text(mapdata1$position,  .7, mapdata1$position,cex.lab = chr.lab )
text(0, labels = c("Chr 2"))

Second level

# plot level 2
mapdata2 <- mapdata[mapdata$chr == 2,]
m <- par()$mar
m[1] <- m[3] <- 0
par(mar=m)
# Set the limits of the  plot
plot(mapdata2$position,mapdata2$position-mapdata1$position, type="n", axes=FALSE, 
xlab="", ylab="Chromsome", yaxt="n" )

polygon(
  c(0,max(mapdata2$position + 0.08 * max(mapdata2$position)),max(mapdata2$position)+  
 0.08 * max(mapdata2$position),0),
  .2*c(-0.3,-0.3,0.3,0.3),
  col= mbar.col
)
segments(mapdata2$position, -.3, mapdata2$position, .3 )
text(mapdata2$position, -.7, mapdata2$snpname, srt = 90, cex.lab = chr.lab)
text(mapdata2$position,  .7, mapdata2$position,cex.lab = chr.lab )
text(0, labels = c("Chr 2"))

Output

(1) How can I automate the process for n levels – extending similar plot to n levels of chr
(2) If you see the barsize with same specification has changed, may be due to different plot area. How can I adjust it so make all plots identical?

Answer 1

ggplot is definitely the way to go here. But if you really want to stick with base plot, then this function would work:

plot.as.stack= function(mapdata1, mbar.col = "blue"){
    # mapdata1 <- mapdata[mapdata$chr == chr,]
    m <- par()$mar
    m[1] <- m[3] <- 0
    par(mar=m)
    # Set the limits of the  plot
    plot(mapdata1$position,mapdata1$position-mapdata1$position, type="n",
       axes=FALSE, 
    xlab="", ylab="Chromsome", yaxt="n" )

    polygon(
      c(0,max(mapdata1$position + 0.08 * max(mapdata1$position)),max(mapdata1$position)+
         0.08 * max(mapdata1$position),0),
      .2*c(-0.3,-0.3,0.3,0.3),
      col= mbar.col
    )
    segments(mapdata1$position, -.3, mapdata1$position, .3 )
    text(mapdata1$position, -.7, mapdata1$snpname, srt = 90, cex.lab = chr.lab)
    text(mapdata1$position,  .7, mapdata1$position,cex.lab = chr.lab )
    text(0, labels = paste("Chr",unique(mapdata1$chr)))
}

# Example Run.
par(mfrow=c(length(unique(mapdata$chr)),1))
x=by(mapdata,factor(mapdata$chr),plot.as.stack) # Assigned to x to prevent output
par(mfrow=c(1,1))

As you can see, I just took your code, put it into a function, and then ran by on it. Note that this would run the function on all of the levels of chr. You could modify it so that the function takes the value of chr instead:

plot.as.stack = function(chr){
    mapdata1 <- mapdata[mapdata$chr == chr,]
    ...
}

And then run the function with values of chr:

par(mfrow=c(5,1))
sapply(1:5,plot.as.stack)
par(mfrow=c(1,1))