The multiple y axes are protecting you in this situation.


z <- cbind(rnorm(100,c(1,10),1), rnorm(100,c(20,30),1))
dotplot(z[,1]+z[,2] ~ facs$Treatment|facs$Sites,
        outer=TRUE,
        scales = list(
          y = list(
            relation="free")),
        ylab=c("y1", "y2"),
        xlab=c("Site 1", "Site 2"),
        strip=FALSE,
        main="problem")

dotplot(z[,1]+z[,2] ~ facs$Treatment|facs$Sites,
        outer=TRUE,
        scales = list(
          y = list(
            relation="free",
            limits=list(c(-5,13),c(-5,13),c(18,32),c(18,32)))),
        ylab=c("y1", "y2"),
        xlab=c("Site 1", "Site 2"),
        strip=FALSE, main="protected")

For more control (such as suppressing the y-tick labels in the right-hand
column,
I recommend Deepayan Sarkar's book.

Rich

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