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I'm very unsure how to plot mixed-level data consisting of a mixture of categorical and continuous predictors, so any help would be appreciated.

This is the data

subject <- factor(rep(c(1,2,3,4,5,6),each=12))
dep <- c(0.3763244126,0.2185001692,0.4191841742,0.9812978664,0.7429273683,0.6254715486,0.6200958213,0.4693300191,0.1779032899,0.0035873980,0.8821949826,0.4818012617,0.0008013437,0.6280700732,0.7126500814,0.4984349359,0.2457996449,0.3085733312,0.5903398243,0.3704800352,0.8215325437,0.0445236221,0.1849731791,0.3670945817,0.0022268933,0.1630332691,0.9734050406,0.2638539758,0.8550054496,0.9413964085,0.4548943471,0.0440815873,0.5222098769,0.6553600784,0.6853486744,0.0571945074,0.0923124240,0.6976544929,0.9257440316,0.5658967043,0.0636543627,0.1038574059,0.0662497468,0.9165439918,0.5200087291,0.9528015053,0.5347318368,0.1848373057,0.9948602219,0.9633110918,0.1482162909,0.9000614029,0.0898618386,0.7975253051,0.8334557347,0.8629821099,0.0001795699,0.2488384889,0.6382902598,0.1103540359,0.2199716354,0.2737281912,0.5694398067,0.7940423761,0.4906677457,0.5191186895,0.4770589883,0.2823238128,0.2458788699,0.6363522802,0.0306954833,0.6979198116)

f1 <- factor(rep(c("Female","Male","Female","Male","Male","Female"), each=12))
f2 <- c(0.098788608,0.934606288,0.145045152,0.841969882,0.498234471,0.562897249,0.359740488,0.082046687,0.183987342,0.082418820,0.173424633,0.799291329,0.041450568,0.686708743,0.352092230,0.823550310,0.650857094,0.331705763,0.659111451,0.745187314,0.066165065,0.870759966,0.154977488,0.031703774,0.065251788,0.707452073,0.564604314,0.224798417,0.656363138,0.047954841,0.500513114,0.923316812,0.706629266,0.561530974,0.670860932,0.414969178,0.709973062,0.452946384,0.187624344,0.278656351,0.562138433,0.655193272,0.014868182,0.518697012,0.414113229,0.273464316,0.844080831,0.962636550,0.952739605,0.728627219,0.761122951,0.309977150,0.755239042,0.208627128,0.481429897,0.376021223,0.753871400,0.164842337,0.921081061,0.859677311,0.600462073,0.119193708,0.276722102,0.854752641,0.962710853,0.956277061,0.228313179,0.920405764,0.001594131,0.104930433,0.241548888,0.549643015)
f3 <- factor(rep(c("day1","day2","day3","day4"),each=3, times=6))

data <- data.frame(sub=subject, dep=dep, f1=f1, f2=f2, f3=f3)

m <- lmer(dep ~ f1*f2*f3 + (1|sub), data=data)

how can I plot the 3-way interaction f1*f2*f3?

I tried using ggplot2 like this

ggplot(aes(x=f2,y=dep,color=f1),data=data) + geom_smooth(method="lm") + facet_grid(".~f3")

but I don't think this is taking into account the fact that this is a mixed-model design, is it?

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    $\begingroup$ Because response variable dep is another dimension, so you need 4-D space to plot 3-way interaction. Maybe you can plot 2-way interaction (f2*f3) at the fixed selected points at another way(f1) such that you can it in 3-D. Do not need to concern about random effect, because all of them f1, f2, f3, are belong to fixed effect. $\endgroup$
    – user158565
    Commented Oct 18, 2018 at 20:39
  • $\begingroup$ Thanks @a_statistician. Sorry for the newbie question, but why don't I need to be concerned about random effects? If I fit an OLS line for each day (which is what my code is doing), this will not be an accurate representation of the mixed model. See my comment below $\endgroup$
    – locus
    Commented Oct 22, 2018 at 19:19
  • $\begingroup$ I mean in the graph do not need to concern random effect.For model, random intercept is needed. $\endgroup$
    – user158565
    Commented Oct 22, 2018 at 19:52

1 Answer 1

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You can specify that you'd like a line for each interaction of f1 and f3 using the group aesthetic and interaction function in R:

ggplot(data, aes(x=f2, y=dep, group = interaction(f1, f3))) +
    geom_smooth(method="lm")

This will create a plot with (in your case 2 * 4 = 8 lines). Then you can use features other than color to distinguish between the factor levels. In your example, you facet, which is OK, but makes it a bit hard to compare the lines. You can also use shape (for points) or line weight / type. Here's an example that uses color for the day and line type for gender:

ggplot(aes(x=f2, y=dep, group = interaction(f1, f3))) + 
    geom_smooth(method="lm", alpha = 0.1, aes(lty=f1, color=f3))

Note that I added alpha = 0.1 to make it a bit easier on the eyes.

enter image description here

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  • $\begingroup$ Nice post! See also Tom Housley's post: tomhouslay.com/2014/09/06/… . $\endgroup$
    – Isabella Ghement
    Commented Oct 19, 2018 at 14:33
  • $\begingroup$ Thanks @Gabe Vacaliuc, the plot looks great. However is this really an accurate depiction of the regression lines of my mixed model? I thought geom_smooth(method="lm") will fit an OLS line for each day, but this is not what the mixed model is doing. see this link and this one $\endgroup$
    – locus
    Commented Oct 22, 2018 at 19:17
  • $\begingroup$ You're right, geom_smooth(method="lm") does not fit a mixed model. I think you'll have to independently calculate the slopes / intercepts as suggested in your second link. $\endgroup$
    – Gabe Vacaliuc
    Commented Oct 23, 2018 at 20:24

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