using ggplot2 to plot mixed effects model

Question

Code below plots random effects from a mixed effects model:

mtcarsSub <- mtcars[,c("wt", "drat", "cyl")]

library(lme4)
mtcarsME <- lmer(drat ~ (1|cyl) + wt, data=mtcarsSub)

mtcarsSub$fixed.effect <- predict(mtcarsME)

library(plyr)
l_ply(list(4, 6, 8), function(x) mtcarsSub[[ paste0("random.effect.cyl", x) ]] <<- mtcarsSub$fixed.effect + ranef(mtcarsME)$cyl[as.character(x),])

library(ggplot2)
ggplot(mtcarsSub, aes(wt, drat, color=factor(cyl))) + 
  geom_point() +
  geom_line(aes(wt, fixed.effect), color="black", size=2) +
  geom_line(aes(wt, random.effect.cyl4), size=2) +
  geom_line(aes(wt, random.effect.cyl6), size=2) +
  geom_line(aes(wt, random.effect.cyl8), size=2)

enter image description here

How can I programatically make each random effect line the same colour as the colours displayed for cyl? Therefore, the random effect line for level 4 of cyl should be red, level 6 of cyl should be green and level 8 of cyl should be blue. I dont want to specify color="red" etc in geom_line().

Didzis Elferts · Accepted Answer · 2013-06-18 16:34:52Z

2

I would suggest to make new data frame for the random effects. For this I use function ldply() and the function you made to calculate random effects for each level. Additionally in this new data frame added column wt and cyl. wt will contain all wt values from mtcarsSub data frame repeated for each level. cyl will contain values 4, 6 and 8.

mt.rand<-ldply(list(4,6,8), function(x) data.frame(
  wt=mtcarsSub$wt,
  cyl=x,
  rand=mtcarsSub$fixed.effect + ranef(mtcarsME)$cyl[as.character(x),]))

Now for the plotting use new data frame in one geom_line() call. As the new data frame also has cyl column it will be assigned the colors as for points.

ggplot(mtcarsSub, aes(wt, drat, color=factor(cyl))) + 
  geom_point() +
  geom_line(aes(wt, fixed.effect), color="black", size=2)+
  geom_line(data=mt.rand,aes(wt,rand),size=2)

edited Jun 18, 2013 at 16:34

answered Jun 18, 2013 at 16:20

Didzis Elferts

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3 Comments

luciano Over a year ago

I've tried your code, but it seems to produce the same plot as in my post. I need every line in the plot to be black

Didzis Elferts Over a year ago

In your question you said that "make each random effect line the same colour as the colours displayed for cyl".

luciano Over a year ago

Apologies yes, answer accepted. Are you able to just delete these comments?

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