[R] Superposing mean line to xyplot

[Deepayan Sarkar]

2011/10/10 Niccolò Bassani <biostatistica at gmail.com>:
> Dear R-users,
> I'm using lattice package and function xyplot for the first time so
> you will excuse me for my inexperience. I'm facing quite a simple
> problem but I'm having troubles on how to solve it, I've read tons of
> old mails in the archives and looked at some slides from Deepayan
> Sarkar but still can not get the point.
>
> This is the context. I've got data on 9 microRNAs, each miRNA has been
> measured on three different arrays and on each array I have 4
> replicates for each miRNA, which sums up to a total of 108
> measurements. I've the suspect that measurement on the first array are
> systematically lower than the others so I wanted to draw some line
> plot where each panel correspond to a miRNA, and each line correspond
> to one of the four replicates (that is: first replicate of miRNA A on
> array 1 must be connected to first replicate of miRNA A on array 2 and
> so on), so that for each panel there are 4 series of three points
> connected by a line/segment. I've done this easily with lattice doing
> this:
>
> array = rep(c("A","B","C"),each = 36) # array replicate
> spot =  rep(1:4,27) # miRNA replicate on each array
> miRNA = rep(rep(paste("miRNA",1:9,sep="."),each=4),3) # miRNA label
> exprs = rnorm(mean=2.8,n = 108) # intensity
> data = data.frame(miRNA,array,spot,exprs)
> xyplot(exprs ~ array|miRNA,data=data,type="b",groups=spot,xlab="Array",ylab
> = "Intensity",col="black",lty=2:5,scales = list(y = list(relation =
> "free")))
>
> Now, I want to superpose to each panel an other series of three points
> connected by a line, where each point represent the mean of the four
> replicates of the miRNA on each array, a sort of mean line. I've tried
> using the following, but it's not working as expected:
>
> xyplot(exprs ~ array|miRNA,data=array,type="b",groups=spot,xlab="Array",ylab
> = "Intensity",col="black",lty=2:5,scales = list(y = list(relation =
> "free")), panel = function(x,y,groups,subscripts){
>        panel.xyplot(x,y,groups=groups,subscripts=subscripts)
>        panel.superpose(x,y,panel.groups=panel.average,groups=groups,subscripts=subscripts)
> })

Is this close to what you are looking for?

xyplot(exprs ~ array | miRNA, data = data, col="black",lty=2:5,
       type="b", groups=spot, xlab="Array",
       ylab = "Intensity",
       scales = list(y = list(relation = "free")),
       panel = function(x, y, groups, subscripts, ...){
           panel.xyplot(x, y, groups=groups, subscripts=subscripts, ...)
           panel.average(x, y, col = "grey", lwd = 2, horizontal = FALSE)
       })

-Deepayan