Question

I have following data and plot:

pos <- rep(1:2000, 20)
xv =c(rep(1:20, each = 2000))
# colrs <- unique(xv)
colrs <- xv # edits 
yv =rnorm(2000*20, 0.5, 0.1)

xv   = lapply(unique(xv), function(x) pos[xv==x])
to.add = cumsum(sapply(xv, max) + 1000)

bp <- c(xv[[1]], unlist(lapply(2:length(xv), function(x) xv[[x]] + to.add[x-1])))
plot (bp,yv, pch = "*", col = colrs)

I have few issues in this plot I could not figure out.

(1) I want to use different color for different group or two different color for different groups (i.e xv), but when I tried color function in terms to be beautiful mixture. Although I need to highlight some points (for example bp 4000 to 4500 for example with blue color)

(2) Instead of bp positions I want to put a tick mark and label with the group.

Thank you, appreciate your help.

Edits: with help of the following answer (with slight different approach in case I have unbalanced number in each group will work) I could get the similar plot. But still question remaining regarding colors is what if I want to use two alternate colors in alternate group ?

Answer 1

You can solve your colour issue by repeating the colour index however many times each group has a point plotted, like so:

plot (bp,yv, pch = "*", col = rep(colrs,each=2000))

The default colour palette (see ?palette or palette() ) will wrap around itself and you might want to specify your own to get 20 distinct colours.

To relabel the x axis, try plotting without the axis and then specifying the points and labels manually.

plot (bp,yv, pch = "*", col = rep(colrs,each=2000),xaxt="n")
axis(1,at=seq(1000,58000,3000),labels=1:20)

If you are trying to squeeze a lot of labels in there, you might have to shrink the text (cex.axis)or spin the labels 90 degrees (las=2).

plot (bp,yv, pch = "*", col = rep(colrs,each=2000),xaxt="n")
axis(1,at=seq(1000,58000,3000),labels=1:20,cex.axis=0.7,las=2)

Result: