How to manipulate y-axis text labels in R varImpPlot? - r

Question

The following sample resembles my dataset:
require(randomForest)
alpha = c(1,2,3,4,5,6)
bravo = c(2,3,4,5,6,7)
charlie = c(2,6,5,3,5,6)
mydata = data.frame(alpha,bravo,charlie)
myrf = randomForest(alpha~bravo+charlie, data = mydata, importance = TRUE)
varImpPlot(myrf, type = 2)
I cannot seem to control the placement of the y-axis labels in varImpPlot. I have tried altering the plot parameters (e.g. mar, oma), with no success. I need the y-axis labels shifted to the left in order to produce a PDF with proper label placement.
How can I shift the y-axis labels to the left?

Answer 1

I tried to use adj parameter but it produces a bug. As varImpPlot , use dotchart behind, Here a version using lattice dotplot. Then you can customize you axs using scales parameters.
imp <- importance(myref, class = NULL, scale = TRUE, type = 2)
dotplot(imp, scales=list(y =list(cex=2,
at = c(1,2),
col='red',
rot =20,
axs='i') ,
x =list(cex=2,col='blue')) )

Answer 2

You can extract the data needed to construct the plot out of myref and construct a plot with ggplot. By doing so you have more freedom in tweaking the plot. Here are some examples
library(ggplot2)
str(myrf)
str(myrf$importance)
data <- as.data.frame(cbind(rownames(myrf$importance),round(myrf$importance[,"IncNodePurity"],1)))
colnames(data) <- c("Parameters","IncNodePurity")
data$IncNodePurity <- as.numeric(as.character(data$IncNodePurity))
Standard plot:
(p <- ggplot(data) + geom_point(aes(IncNodePurity,Parameters)))
Rotate y-axis labels:
(p1 <- p+ theme(axis.text.y = element_text(angle = 90, hjust = 1)))
Some more tweaking (also first plot shown here):
(p2 <- p1 + scale_x_continuous(limits=c(3,7),breaks=3:7) + theme(axis.title.y = element_blank()))
Plot that looks like the varImpPlot (second plot shown here) :
(p3 <- p2+ theme(panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
panel.grid.minor.y = element_blank(),
panel.grid.major.y = element_line(colour = 'gray', linetype = 'dashed'),
panel.background = element_rect(fill='white', colour='black')))
Saving to pdf is easy with ggplot:
ggsave("randomforestplot.pdf",p2)
or
ggsave("randomforestplot.png",p2)
p2
p3

Answer 3

Did I understood correctly, that you want to get texts charlie and bravo more left of the boundary of the plot? If so, here's one hack to archive this, based on the modification of the rownames used in plotting:
myrf = randomForest(alpha~bravo+charlie, data = mydata, importance = TRUE)
#add white spaces at the end of the rownames
rownames(myrf$importance)<-paste(rownames(myrf$importance), " ")
varImpPlot(myrf, type = 2)
The adj parameter in dotchart is fixed as 0 (align to right), so that cannot be changed without modifying the code of dotchart:
mtext(labs, side = 2, line = loffset, at = y, **adj = 0**, col = color,
las = 2, cex = cex, ...)
(from dotchart)
EDIT:
You can make another type of hack also. Take the code of dotchart, change the above line to
mtext(labs, side = 2, line = loffset, at = y, adj = adjust_ylab, col = color,
las = 2, cex = cex, ...)
Then add argument adjust_ylab to the argument list, and rename the function as for example dotchartHack. Now copy the code of varImpPlot, find the line which calls dotchart, change the function name to dotchartHack and add the argument adjust_ylab=adjust_ylab to function call, rename the function to varImpPlotHack and add adjust_ylab to this functions argument list. Now you can change the alignment of the charlie and bravo by changing the parameter adjust_ylab:
myrf = randomForest(alpha~bravo+charlie, data = mydata, importance = TRUE)
varImpPlotHack(myrf, type = 2,adjust_ylab=0.5)
From ?par:
The value of adj determines the way in which text strings are
justified in text, mtext and title. A value of 0 produces
left-justified text, 0.5 (the default) centered text and
right-justified text. (Any value in [0, 1] is allowed, and on most
devices values outside that interval will also work.)