Wrong coordinates in R plot (package e1071)

Question

I'm trying to add single point to plot.tune but it ends up in a wrong place. I'm calling

plot(radial.tune2, color.palette = topo.colors)
points(radial.tune2$best.parameters, pch=20, col='red')

where radial.tune2 is tune object. The parameters are as follows:

> radial.tune2$best.parameters
    cost   gamma
52 0.385 0.04125

I think this is due to the fact, that the scale bar is not taken into account (as I re-scaled the plot, the red dot appeared in different places relative to axes).

I looked into documentation, but found nothing about adding points to plots of tune object. I found this question which seems to have similar origin, but does not address the problem properly.

Edit: here is simplified example of the same problem. It produces different plot, but with the same shifting-to-the-right property.

library(mlbench)
library(e1071)

data(BreastCancer)
BreastCancer$Id <- NULL
BreastCancer <- na.omit(BreastCancer)
data <- as.data.frame(lapply(BreastCancer, as.numeric))
data$Class <- BreastCancer$Class
names(data) <- names(BreastCancer)

C.range <- seq(0.1, 0.7, by=0.05)
gamma.range <- seq(0.001, 0.30, by=0.05)

set.seed(1)
radial.tune <- tune(svm, train.x=data[,-10], # 10 -> Class
                    train.y=data[,"Class"],
                    kernel="radial",
                    ranges=list(cost=C.range, gamma=gamma.range),
                    tunecontrol=tune.control(sampling="bootstrap"))

plot(radial.tune, color.palette = topo.colors)
points(radial.tune$best.parameters, pch=20, col='red')

Could you please share some reproducible data using `dput`? – Quinten Jan 28 '23 at 13:46 — Quinten, Jan 28 '23 at 13:46
Specify x and y separately in `points`. – Roland Jan 28 '23 at 15:13 — Roland, Jan 28 '23 at 15:13
@Roland it does not change anything. – Esgeriath Jan 28 '23 at 15:16 — Esgeriath, Jan 28 '23 at 15:16

score 0 · Accepted Answer · answered Jan 28 '23 at 17:08

0

I found out that this is actually problem of filled.countour which is being called under the hood. See this thread for more info.

answered Jan 28 '23 at 17:08

Esgeriath

111
5

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Wrong coordinates in R plot (package e1071)

1 Answers1