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I was wondering if someone could help me with something. I have a mixed effects model fitted with lme4 and I have extracted the random effects to plot in a dotplot. I have followed the very helpful code pasted below and have got the plot shown. However, I would like to be able to tidy up the x-axis scales a bit to make it look a bit tidier. Ideally I want axis tick labels at -0.1, 0.1 and 0.3. I have tried modifying the function with scale_x_continous in various places but as I am not entirely sure how the whole code works together I don't quite know where this would go or if this would even work. I would be very grateful for any assitance, thank you.

## re = object of class ranef.mer
ggCaterpillar <- function(re, QQ=TRUE, likeDotplot=TRUE) {
require(ggplot2)
f <- function(x) {
pv   <- attr(x, "postVar")
cols <- 1:(dim(pv)[1])
se   <- unlist(lapply(cols, function(i) sqrt(pv[i, i, ])))
ord  <- unlist(lapply(x, order)) + rep((0:(ncol(x) - 1)) * nrow(x), each=nrow(x))
pDf  <- data.frame(y=unlist(x)[ord],
                   ci=1.96*se[ord],
                   nQQ=rep(qnorm(ppoints(nrow(x))), ncol(x)),
                   ID=factor(rep(rownames(x), ncol(x))[ord], levels=rownames(x)[ord]),
                   ind=gl(ncol(x), nrow(x), labels=names(x)))

if(QQ) {  ## normal QQ-plot
  p <- ggplot(pDf, aes(nQQ, y)) + scale_x_continous(limits=c(-0.6,0.7), breaks=seq(-0.6,0.7, by=0.1), labels=c("-0.6","-0.5","-0.4","0.3","0.2","0.1","0.0", "0.1", "0.2", "0.3", "0.4", "0.5", "0.6", "0.7"))
  p <- p + facet_wrap(~ ind, scales="free")
  p <- p + xlab("Standard normal quantiles") + ylab("Random effect quantiles")
} else {  ## caterpillar dotplot
  p <- ggplot(pDf, aes(ID, y)) + coord_flip()
  if(likeDotplot) {  ## imitate dotplot() -> same scales for random effects
    p <- p + facet_wrap(~ ind)
  } else {           ## different scales for random effects
    p <- p + facet_grid(ind ~ ., scales="free_y")
  }
  p <- p + xlab("Levels") + ylab("Random effects")
}

p <- p + theme(legend.position="none")
p <- p + geom_hline(yintercept=0)
p <- p + geom_errorbar(aes(ymin=y-ci, ymax=y+ci), width=0, colour="black")
p <- p + geom_point(aes(size=1.2), colour="blue") 
return(p)
#plotting the dotplot of my model
ggCaterpillar(ranef(model, condVar=TRUE), QQ=FALSE)

My dotplot

LauRa28
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  • `p + scale_x_continuous(breaks=seq(-0.3,0.3,0.1))`. – eipi10 Apr 20 '17 at 15:21
  • Thank you, I have tried this but I got the following error message: Error: Discrete value supplied to continuous scale. Do you know why this might be? – LauRa28 Apr 20 '17 at 15:25
  • I just tried p + scale_y_continuous(breaks=seq(-0.3, 0.3, 0.1))and this worked! I think this may have something to do with the plot coordinates being flipped. @eipi10 – LauRa28 Apr 20 '17 at 15:44
  • Sorry, I didn't notice the `coord_flip` in your code. The horizontal axis in your plot is actually the "y-axis", so `scale_y_continuous` is the appropriate command to adjust the axis breaks. – eipi10 Apr 20 '17 at 15:46
  • Yes just figured it out too, thank you! How do I accept your answer @eipi10? – LauRa28 Apr 20 '17 at 15:48
  • Questions like this have been asked before, so I'm pretty sure this is a duplicate. No need for me to add this as an answer. – eipi10 Apr 20 '17 at 15:54

0 Answers0