[R] Extract hyperplane from kernlab's Support Vector Machine model
Luigi Marongiu
m@rong|u@|u|g| @end|ng |rom gm@||@com
Wed May 8 10:25:21 CEST 2019
Dear all,
I would like to extract an hyperplance froma SVM model generated with
the kernlab package. The model I have made is non-linear and I am
looking to plot the line that separates the two groups in order to
draw custom plots with more control.
I understand that I should use a contour plot but I do not understand
how to implement the function.
I will show the process I have done with the example reported in here
(https://www.datacamp.com/community/tutorials/support-vector-machines-r);
I had to re-arrange the data to pass from e1071 to kernlab.
Essentially it all works until I reach the contour part. How can I add
a line that represents the boundaries between the red and blue dots?
In the following working example, this boundary (the hyperplane) is
represented roughly by the green line; in the real case, it should be
a convoluted curve.
Also, I reckon countour should have an add=TRUE option in order to add
it to an existing plot.
Thank you
>>>
set.seed(10111)
library(kernlab)
x = matrix(rnorm(40), 20, 2)
y = rep(c(-1, 1), c(10, 10))
x[y == 1,] = x[y == 1,] + 1
plot(x, col = y + 3, pch = 19)
dat = data.frame(x, y = as.factor(y))
MAXx1 = max(dat$X1)
MAXx2 = max(dat$X2)
MINx1 = min(dat$X1)
MINx2 = min(dat$X2)
svmfit = ksvm(y ~ X1+X2, data = dat,
type = "C-svc",
kernel = "vanilladot",
kpar = "automatic",
C = 10,
prob.model = TRUE)
print(svmfit)
plot(svmfit, data = dat)
# make own plot
make.grid = function(x, n = 75) {
grange = apply(x, 2, range)
x1 = seq(from = grange[1,1], to = grange[2,1], length = n)
x2 = seq(from = grange[1,2], to = grange[2,2], length = n)
expand.grid(X1 = x1, X2 = x2)
}
M = matrix(c(dat$X1, dat$X2), ncol = 2, byrow=FALSE)
xgrid = make.grid(M)
xgrid[1:10,]
ygrid = predict(svmfit, xgrid)
plot(xgrid, col = c("red","blue")[as.numeric(ygrid)], pch = 20, cex = .2,
xlim=c(MINx1, MAXx1), ylim = c(MINx2, MAXx2))
points(dat[dat[, "y"] == -1,], col = "red", pch = 19)
points(dat[dat[, "y"] == 1,], col = "blue", pch = 18, cex = 1.5)
abline(a = 0.9, b = -0.65, col = "green", lwd = 2)
# here is where I am lost
contour(dat[dat[, "y"] == -1,]$X1, dat[dat[, "y"] == 1,]$X2,
dat[dat[, "y"] == -1,]$y)
# Error in contour.default(dat[dat[, "y"] == -1, ]$X1, dat[dat[, "y"] == :
# increasing 'x' and 'y' values expected
M_ord = M[order(M[,1], M[,2],decreasing=TRUE),]
contour(M[, 1], M[, 2], dat[dat[, "y"] == -1,]$y)
# Error in contour.default(M[, 1], M[, 2], dat[dat[, "y"] == -1, ]$y) :
# increasing 'x' and 'y' values expected
M_ord = M[order(M[,1], M[,2],decreasing=FALSE),]
contour(M[, 1], M[, 2], dat[dat[, "y"] == -1,]$y)
# Error in contour.default(M[, 1], M[, 2], dat[dat[, "y"] == -1, ]$y) :
# increasing 'x' and 'y' values expected
--
Best regards,
Luigi
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