gam plots with ggplot

Question

I need to create some gam plots in ggplot. I can do them with the general plot function, but am unsure how to do with ggplot. Here is my code and plots with the regular plot function. I'm using the College data set from the ISLR package.

train.2 <- sample(dim(College)[1],2*dim(College)[1]/3)
train.college <- College[train.2,]
test.college <- College[-train.2,]
gam.college <- gam(Outstate~Private+s(Room.Board)+s(Personal)+s(PhD)+s(perc.alumni)+s(Expend)+s(Grad.Rate), data=train.college)
par(mfrow=c(2,2))
plot(gam.college, se=TRUE,col="blue")

See help("plot.gam") and look under *Value* there. – Roland Mar 25 '18 at 08:06 — Roland, Mar 25 '18 at 08:06

missuse · Accepted Answer · 2020-01-08T10:02:43.740

See update below old answer.

Old answer:

There is an implementation of GAM plotting using ggplot2 in voxel library. Here is how you would go about it:

library(ISLR)
library(mgcv)
library(voxel)
library(tidyverse)
library(gridExtra)
data(College)

set.seed(1)
train.2 <- sample(dim(College)[1],2*dim(College)[1]/3)
train.college <- College[train.2,]
test.college <- College[-train.2,]
gam.college <- gam(Outstate~Private+s(Room.Board)+s(Personal)+s(PhD)+s(perc.alumni)+s(Expend)+s(Grad.Rate), data=train.college)

vars <- c("Room.Board", "Personal", "PhD", "perc.alumni","Expend", "Grad.Rate")

map(vars, function(x){
  p <- plotGAM(gam.college, smooth.cov = x) #plot customization goes here
  g <- ggplotGrob(p)
}) %>%
  {grid.arrange(grobs = (.), ncol = 2, nrow = 3)}

after a bunch of errors: In plotGAM(gam.college, smooth.cov = x) : There are one or more factors in the model fit, please consider plotting by group since plot might be unprecise

To compare to the plot.gam:

par(mfrow=c(2,3))
plot(gam.college, se=TRUE,col="blue")

You might also want to plot the observed values:

map(vars, function(x){
  p <- plotGAM(gam.college, smooth.cov = x) +
    geom_point(data = train.college, aes_string(y = "Outstate", x = x ), alpha = 0.2) +
    geom_rug(data = train.college, aes_string(y = "Outstate", x = x ), alpha = 0.2)
  g <- ggplotGrob(p)
}) %>%
  {grid.arrange(grobs = (.), ncol = 3, nrow = 2)}

or per group (especially important if you used the by argument (interaction in gam).

map(vars, function(x){
  p <- plotGAM(gam.college, smooth.cov = x, groupCovs = "Private") +
    geom_point(data = train.college, aes_string(y = "Outstate", x = x, color= "Private"), alpha = 0.2) +
    geom_rug(data = train.college, aes_string(y = "Outstate", x = x, color= "Private"  ), alpha = 0.2) +
    scale_color_manual("Private", values = c("#868686FF", "#0073C2FF")) +
    theme(legend.position="none")
  g <- ggplotGrob(p)
}) %>%
  {grid.arrange(grobs = (.), ncol = 3, nrow = 2)}

Update, 08. Jan. 2020.

I currently think the package mgcViz offers superior functionality compared to the voxel::plotGAMfunction. An example using the above data set and models:

library(mgcViz)
viz <- getViz(gam.college)
print(plot(viz, allTerms = T), pages = 1)

plot customization is similar go ggplot2 syntax:

trt <- plot(viz, allTerms = T) +
  l_points() +
  l_fitLine(linetype = 1)  +
  l_ciLine(linetype = 3) +
  l_ciBar() +
  l_rug() +
  theme_grey() 

print(trt, pages = 1)

This vignette shows many more examples.

I'm getting this error after running that code. Error in plotGAM(gam.college, smooth.cov = x) : gamFit is not a object of type gam — Marvin Bahr, Mar 25 '18 at 14:08
What library is the `gam` method you are using? If you could swap to `library(mgcv)` and `mgcv::gam` it would probably work. — missuse, Mar 25 '18 at 14:11
@missuse, is it possible to plot two different models on the same plot, one for each level of 'Private', instead of using the interaction? — fibar, Aug 03 '18 at 11:25
@fibar Yes. generate two models, then generate two plots and then combine in one plot using `gridExtra`, `cowplot` or any of the other few packages ment for this sort of thing. — missuse, Aug 03 '18 at 11:38
@misuse I noticed that `plotGAM` and `plot` have different y axis. The y axis in `plotGAM` is predicted value of dependent variable. What does the y axis in `plot` mean? Their values are not the same (e.g., _8000~16000_ V.S. _-6000~6000_ ). — T X, Apr 09 '19 at 06:06
@T X good catch. Here is an answer addressing this: https://stackoverflow.com/questions/15764810/changing-the-y-axis-of-default-plot-gam-graphs. When I get some time to research I will edit the answer. — missuse, Apr 09 '19 at 08:57
Interestingly the gam model fitted now is different then the one fitted when the answer was posted using the same code. — missuse, Apr 09 '19 at 09:03

gam plots with ggplot

1 Answers1

See update below old answer.

Old answer:

Update, 08. Jan. 2020.