Interaction Plot in ggplot2

Question

I'm trying to make interaction plot with ggplot2. My code is below:

library(ggplot2)
p <- qplot(as.factor(dose), len, data=ToothGrowth, geom = "boxplot", color = supp) + theme_bw()
p <- p + labs(x="Dose", y="Response")
p <- p + stat_summary(fun.y = mean, geom = "point", color = "blue")
p <- p + stat_summary(fun.y = mean, geom = "line", aes(group = 1))
p <- p  + opts(axis.title.x = theme_text(size = 12, hjust = 0.54, vjust = 0))
p <- p  + opts(axis.title.y = theme_text(size = 12, angle = 90,  vjust = 0.25))
print(p)

How can I plot dose-supp level combination means rather than only dose level means which I'm getting here? Thanks in advance for your help.

enter image description here

joran · Accepted Answer · 2011-09-06 16:50:28Z

32

You can precalculate the values in their own data frame:

toothInt <- ddply(ToothGrowth,.(dose,supp),summarise, val = mean(len))

ggplot(ToothGrowth, aes(x = factor(dose), y = len, colour = supp)) + 
    geom_boxplot() + 
    geom_point(data = toothInt, aes(y = val)) +
    geom_line(data = toothInt, aes(y = val, group = supp)) + 
    theme_bw()

enter image description here

Note that using ggplot rather than qplot makes the graph construction a lot clearer for more complex plots like these (IMHO).

answered Sep 6, 2011 at 16:50

joran

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Community · Accepted Answer · 2017-05-23 12:00:28Z

9

You can compute your summaries by the appropriate groups (supp):

p <- qplot(as.factor(dose), len, data=ToothGrowth, geom = "boxplot", color = supp) + theme_bw()
p <- p + labs(x="Dose", y="Response")
p <- p + stat_summary(fun.y = mean, geom = "point", color = "blue", aes(group=supp))
p <- p + stat_summary(fun.y = mean, geom = "line", aes(group = supp))
p <- p  + opts(axis.title.x = theme_text(size = 12, hjust = 0.54, vjust = 0))
p <- p  + opts(axis.title.y = theme_text(size = 12, angle = 90,  vjust = 0.25))
print(p)

Or converting to ggplot syntax (and combining into one expression)

ggplot(ToothGrowth, aes(as.factor(dose), len, colour=supp)) +
  geom_boxplot() +
  stat_summary(aes(group=supp), fun.y = mean, geom="point", colour="blue") +
  stat_summary(aes(group=supp), fun.y = mean, geom="line") +
  scale_x_discrete("Dose") +
  scale_y_continuous("Response") +
  theme_bw() +
  opts(axis.title.x = theme_text(size = 12, hjust = 0.54, vjust = 0),
    axis.title.y = theme_text(size = 12, angle = 90,  vjust = 0.25))

EDIT:

To make this work with 0.9.3, it effectively becomes Joran's answer.

library("plyr")
summ <- ddply(ToothGrowth, .(supp, dose), summarise, len = mean(len))

ggplot(ToothGrowth, aes(as.factor(dose), len, colour=supp)) +
  geom_boxplot() +
  geom_point(data = summ, aes(group=supp), colour="blue", 
             position = position_dodge(width=0.75)) +
  geom_line(data = summ, aes(group=supp), 
            position = position_dodge(width=0.75)) +
  scale_x_discrete("Dose") +
  scale_y_continuous("Response") +
  theme_bw() +
  theme(axis.title.x = element_text(size = 12, hjust = 0.54, vjust = 0),
        axis.title.y = element_text(size = 12, angle = 90,  vjust = 0.25))

enter image description here

edited May 23, 2017 at 12:00

CommunityBot

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answered Sep 6, 2011 at 18:49

Brian Diggs

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3 Comments

MYaseen208 Over a year ago

Thanks Brian Diggs for your reply. How to put different colors for dot points for means?

Brian Diggs Over a year ago

For the points, the default mapping of the color was overridden to be "blue", so just remove colour="blue" from that stat_summary call, and it will default back to being mapped based on the supp variable.

hpesoj626 Over a year ago

This is the best answer.

Bryan Hanson · Accepted Answer · 2011-09-06 21:53:55Z

7

If you think you might need a more general approach, you could try function rxnNorm in package HandyStuff (github.com/bryanhanson/HandyStuff). Disclaimer: I'm the author. Disclaimer #2: the box plot option doesn't quite work right, but all the other options are fine.

Here's an example using the ToothGrowth data:

p <- rxnNorm(data = ToothGrowth, res = "len", fac1 = "dose", fac2 = "supp", freckles = TRUE, method = "iqr", fac2cols = c("red", "green"))
print(p)

rxnNorm Demo

answered Sep 6, 2011 at 21:53

Bryan Hanson

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Junbo Huang · Accepted Answer · 2016-10-16 18:20:40Z

1

a much easier way. without ddply. directly with ggplot2.

ggplot(ToothGrowth, aes(x = factor(dose) , y=len , group = supp, color = supp)) + 
  geom_boxplot() +
  geom_smooth(method = lm, se=F) +
  xlab("dose") +
  ylab("len")

answered Oct 16, 2016 at 18:20

Junbo Huang

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1 Comment

hpesoj626 Over a year ago

This correctly draws the lines but not the boxplots.

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