使用ggplot绘制gam图

Question

我需要在ggplot中创建一些gam图。我可以用一般的plot函数来做这些事情，但是我不确定如何使用ggplot。下面是我的代码和使用常规plot函数绘制的图。我使用的是ISLR包中的学院数据集。

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")

Answer 1

请参阅旧答案下面的更新。

老生常谈：

在voxel库中有一个使用ggplot2实现GAM绘图的方法。下面是你该怎么做的：

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)}

在一堆错误之后：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

​

​

与plot.gam进行比较

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

​

​

您可能还希望绘制观察值：

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)}

​

​

或每个组(如果您使用by参数(gam中的交互)，则尤其重要。

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)}

​

​

更新时间: 2020年1月8日

我目前认为与voxel::plotGAM函数相比，mgcViz包提供了更好的功能。使用上述数据集和模型的示例：

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

​

​

绘图定制类似于go ggplot2语法：

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)

​

​

这个vignette展示了更多的例子。