Untitled

Plotting a rather complex chart using R and axis break()
set.seed(1)
    # make data.frame just with info for the lines you'll actually draw
    # your data was mostly zeros, no need for those lines
    position <- sort(sample(1:4563,45,replace = FALSE))
    # but the x position needs to be shaved down!
    # modulars are the real x positions on the plot:
    xpos <- position%%600
    # line direction appeared in your example but not in your text
    posorneg <- sample(c(-1,1),45,replace = TRUE,prob=c(.05,.95))
    # oxidant concentration for line width- just rescale the oxidant concentration
    # values you have to fall between say .5 and 3, or whatever is nice and visible
    oxconc   <- (.5+runif(45))^2
    # oxidant type determines line type- you mention 2
    # just assign these types to lines types (integers in R)
    oxitype  <- sample(c(1,2),45,replace = TRUE)
    # let's say there's another dimension you want to map color to
    # in your example png, but not in your description.
    color <- sample(c("green","black","blue"),45,replace=TRUE)

    # and finally, which level does each segment need to belong to?
    # you have 8 line levels in your example png. This works, might take
    # some staring though:
    level <- 0
    for (i in 0:7){
    level[position %in% ((i*600):(i*600+599))] <- 8-i
    }

    # now stick into data.drame:
    AminoData <-data.frame(position = position, xpos = xpos, posorneg = posorneg,
         oxconc = oxconc, oxitype = oxitype, level = level, color = color)

# now we draw the base plot:
    par(mar=c(3,3,3,3))
    plot(NULL, type = "n", axes = FALSE, xlab = "", ylab = "",
         ylim =  c(0,9), xlim = c(-10,609))
    # horizontal segments:
    segments(0,1:8,599,1:8,gray(.5))
    # some ticks: (also not pretty)
    segments(rep(c((0:5)*100,599),8), rep(1:8,each=7)-.05, rep(c((0:5)*100,599),8),
       rep(1:8,each=7)+.05, col=gray(.5))
    # label endpoints:
    text(rep(10,8)+.2,1:8-.2,(7:0)*600,pos=2,cex=.8)
    text(rep(589,8)+.2,1:8-.2,(7:0)*600+599,pos=4,cex=.8)
    # now the amino line segments, remember segments() is vectorized
    segments(AminoData$xpos, AminoData$level, AminoData$xpos,
       AminoData$level + .5 * AminoData$posorneg, lty = AminoData$oxitype,
       lwd = AminoData$oxconc, col = as.character(AminoData$color))
    title("mostly you just need to reshape and preparenyour data to do this easily in base")