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R plot gam 3D surface to show also actual response values



2019 Community Moderator ElectionRough thin-plate spline fitting (thin-plate spline interpolation) in R with mgcvggplot2 geom_rug rescales unused axes - how do I stop this?ggplot confidence bands from gam predict$fit and predict$se.fitR: adding droplines to fitted plane in 3D scatterplot in rgl“Cut out” 3D Surface Plot in RSwapping axes for a 2-predictor GAM in rPredict values from multivariate linear modelR: Plotting “Actual vs. Fitted”How to plot raw and predict values for 2x2x2 time-series in R?Is it possible to specify lower bound in response variable during smooth with gam?R - GAM regressions (mgcv) response curves change shape/direction when adding new variables










0















I'm quite an R newbie and facing the following challange.
I'll share my code here but applied to a different dataframe since I cannot share the original dataframe.
This is my code:



fit = gam( carb ~ te(cyl, hp, k=c(3,4)), data = mtcars)
plot(fit,rug=F,pers=T,theta=45,main="test")


using my company's data, this generates a nice surface with the predicted values on the Z axes.
I would like to add the actual response values as red dots on Z axis so that I could see where predicted values are under/over estimating the actual reponse.
Would you know what parameter I should add to plot in order to do that?
Many thanks










share|improve this question
























  • That's not easy. The plot function uses persp to draw the surface. persp returns enough information to add points, but the plot function doesn't save it.

    – user2554330
    Mar 7 at 16:39











  • This Q&A contains code to guide you how to do this. You need to call predict.gam, perps, trans3d, points and segments. Working with plot.gam is not a good idea because smooth functions are centered, and it would be hard for you to work out the vertical shift correctly.

    – 李哲源
    Mar 7 at 16:54











  • @李哲源 which Q&A are you referring to?

    – Angelo
    Mar 7 at 17:20











  • @Angelo Oh I did not link it! Sorry, here it is: stackoverflow.com/q/52279218/4891738

    – 李哲源
    Mar 7 at 17:28











  • @李哲源: Nice! You should write this up as an answer: I don't think the question is a duplicate of the linked one.

    – user2554330
    Mar 7 at 17:34















0















I'm quite an R newbie and facing the following challange.
I'll share my code here but applied to a different dataframe since I cannot share the original dataframe.
This is my code:



fit = gam( carb ~ te(cyl, hp, k=c(3,4)), data = mtcars)
plot(fit,rug=F,pers=T,theta=45,main="test")


using my company's data, this generates a nice surface with the predicted values on the Z axes.
I would like to add the actual response values as red dots on Z axis so that I could see where predicted values are under/over estimating the actual reponse.
Would you know what parameter I should add to plot in order to do that?
Many thanks










share|improve this question
























  • That's not easy. The plot function uses persp to draw the surface. persp returns enough information to add points, but the plot function doesn't save it.

    – user2554330
    Mar 7 at 16:39











  • This Q&A contains code to guide you how to do this. You need to call predict.gam, perps, trans3d, points and segments. Working with plot.gam is not a good idea because smooth functions are centered, and it would be hard for you to work out the vertical shift correctly.

    – 李哲源
    Mar 7 at 16:54











  • @李哲源 which Q&A are you referring to?

    – Angelo
    Mar 7 at 17:20











  • @Angelo Oh I did not link it! Sorry, here it is: stackoverflow.com/q/52279218/4891738

    – 李哲源
    Mar 7 at 17:28











  • @李哲源: Nice! You should write this up as an answer: I don't think the question is a duplicate of the linked one.

    – user2554330
    Mar 7 at 17:34













0












0








0








I'm quite an R newbie and facing the following challange.
I'll share my code here but applied to a different dataframe since I cannot share the original dataframe.
This is my code:



fit = gam( carb ~ te(cyl, hp, k=c(3,4)), data = mtcars)
plot(fit,rug=F,pers=T,theta=45,main="test")


using my company's data, this generates a nice surface with the predicted values on the Z axes.
I would like to add the actual response values as red dots on Z axis so that I could see where predicted values are under/over estimating the actual reponse.
Would you know what parameter I should add to plot in order to do that?
Many thanks










share|improve this question
















I'm quite an R newbie and facing the following challange.
I'll share my code here but applied to a different dataframe since I cannot share the original dataframe.
This is my code:



fit = gam( carb ~ te(cyl, hp, k=c(3,4)), data = mtcars)
plot(fit,rug=F,pers=T,theta=45,main="test")


using my company's data, this generates a nice surface with the predicted values on the Z axes.
I would like to add the actual response values as red dots on Z axis so that I could see where predicted values are under/over estimating the actual reponse.
Would you know what parameter I should add to plot in order to do that?
Many thanks







r rgl gam






share|improve this question















share|improve this question













share|improve this question




share|improve this question








edited Mar 7 at 20:01









user2554330

9,98211241




9,98211241










asked Mar 7 at 15:28









AngeloAngelo

7510




7510












  • That's not easy. The plot function uses persp to draw the surface. persp returns enough information to add points, but the plot function doesn't save it.

    – user2554330
    Mar 7 at 16:39











  • This Q&A contains code to guide you how to do this. You need to call predict.gam, perps, trans3d, points and segments. Working with plot.gam is not a good idea because smooth functions are centered, and it would be hard for you to work out the vertical shift correctly.

    – 李哲源
    Mar 7 at 16:54











  • @李哲源 which Q&A are you referring to?

    – Angelo
    Mar 7 at 17:20











  • @Angelo Oh I did not link it! Sorry, here it is: stackoverflow.com/q/52279218/4891738

    – 李哲源
    Mar 7 at 17:28











  • @李哲源: Nice! You should write this up as an answer: I don't think the question is a duplicate of the linked one.

    – user2554330
    Mar 7 at 17:34

















  • That's not easy. The plot function uses persp to draw the surface. persp returns enough information to add points, but the plot function doesn't save it.

    – user2554330
    Mar 7 at 16:39











  • This Q&A contains code to guide you how to do this. You need to call predict.gam, perps, trans3d, points and segments. Working with plot.gam is not a good idea because smooth functions are centered, and it would be hard for you to work out the vertical shift correctly.

    – 李哲源
    Mar 7 at 16:54











  • @李哲源 which Q&A are you referring to?

    – Angelo
    Mar 7 at 17:20











  • @Angelo Oh I did not link it! Sorry, here it is: stackoverflow.com/q/52279218/4891738

    – 李哲源
    Mar 7 at 17:28











  • @李哲源: Nice! You should write this up as an answer: I don't think the question is a duplicate of the linked one.

    – user2554330
    Mar 7 at 17:34
















That's not easy. The plot function uses persp to draw the surface. persp returns enough information to add points, but the plot function doesn't save it.

– user2554330
Mar 7 at 16:39





That's not easy. The plot function uses persp to draw the surface. persp returns enough information to add points, but the plot function doesn't save it.

– user2554330
Mar 7 at 16:39













This Q&A contains code to guide you how to do this. You need to call predict.gam, perps, trans3d, points and segments. Working with plot.gam is not a good idea because smooth functions are centered, and it would be hard for you to work out the vertical shift correctly.

– 李哲源
Mar 7 at 16:54





This Q&A contains code to guide you how to do this. You need to call predict.gam, perps, trans3d, points and segments. Working with plot.gam is not a good idea because smooth functions are centered, and it would be hard for you to work out the vertical shift correctly.

– 李哲源
Mar 7 at 16:54













@李哲源 which Q&A are you referring to?

– Angelo
Mar 7 at 17:20





@李哲源 which Q&A are you referring to?

– Angelo
Mar 7 at 17:20













@Angelo Oh I did not link it! Sorry, here it is: stackoverflow.com/q/52279218/4891738

– 李哲源
Mar 7 at 17:28





@Angelo Oh I did not link it! Sorry, here it is: stackoverflow.com/q/52279218/4891738

– 李哲源
Mar 7 at 17:28













@李哲源: Nice! You should write this up as an answer: I don't think the question is a duplicate of the linked one.

– user2554330
Mar 7 at 17:34





@李哲源: Nice! You should write this up as an answer: I don't think the question is a duplicate of the linked one.

– user2554330
Mar 7 at 17:34












1 Answer
1






active

oldest

votes


















2














As @李哲源 pointed out in the comments, you shouldn't use plot here, because it's not flexible enough. Here's a version based on the referenced question Rough thin-plate spline fitting (thin-plate spline interpolation) in R with mgcv.



# First, get the fit
library(mgcv)
fit <- gam( carb ~ te(cyl, hp, k=c(3,4)), data = mtcars)

# Now expand it to a grid so that persp will work
steps <- 30
cyl <- with(mtcars, seq(min(cyl), max(cyl), length = steps) )

hp <- with(mtcars, seq(min(hp), max(hp), length = steps) )
newdat <- expand.grid(cyl = cyl, hp = hp)
carb <- matrix(predict(fit, newdat), steps, steps)

# Now plot it
p <- persp(cyl, hp, carb, theta = 45, col = "yellow")

# To add the points, you need the same 3d transformation
obs <- with(mtcars, trans3d(cyl, hp, carb, p))
pred <- with(mtcars, trans3d(cyl, hp, fitted(fit), p))
points(obs, col = "red", pch = 16)

# Add segments to show where the points are in 3d
segments(obs$x, obs$y, pred$x, pred$y)


That produces the following plot:



screen shot



You might not want to make predictions so far from the observed data. You can put NA values into carb to avoid that. This code does that:



exclude <- exclude.too.far(rep(cyl,steps), 
rep(hp, rep(steps, steps)),
mtcars$cyl,
mtcars$hp, 0.15) # 0.15 chosen by trial and error
carb[exclude] <- NA
p <- persp(cyl, hp, carb, theta = 45, col = "yellow")
obs <- with(mtcars, trans3d(cyl, hp, carb, p))
pred <- with(mtcars, trans3d(cyl, hp, fitted(fit), p))
points(obs, col = "red", pch = 16)
segments(obs$x, obs$y, pred$x, pred$y)


That produces this plot:



screen shot



Finally, you might want to use the rgl package to get a dynamic graph instead. After the same manipulations as above, use this code to do the plotting:



library(rgl)
persp3d(cyl, hp, carb, col="yellow", polygon_offset = 1)
surface3d(cyl, hp, carb, front = "lines", back = "lines")
with(mtcars, points3d(cyl, hp, carb, col = "red"))
with(mtcars, segments3d(rep(cyl, each = 2),
rep(hp, each = 2),
as.numeric(rbind(fitted(fit),
carb))))


Here's one possible view:



screen shot



You can use the mouse to rotate this one if you want to see it from a different angle. One other advantage is that points that should be hidden by the surface really are hidden; in persp, they'll plot on top even if they should be behind it.






share|improve this answer























  • Absolutely fantastic answer. You made my day. Thank you so much

    – Angelo
    yesterday










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1 Answer
1






active

oldest

votes








1 Answer
1






active

oldest

votes









active

oldest

votes






active

oldest

votes









2














As @李哲源 pointed out in the comments, you shouldn't use plot here, because it's not flexible enough. Here's a version based on the referenced question Rough thin-plate spline fitting (thin-plate spline interpolation) in R with mgcv.



# First, get the fit
library(mgcv)
fit <- gam( carb ~ te(cyl, hp, k=c(3,4)), data = mtcars)

# Now expand it to a grid so that persp will work
steps <- 30
cyl <- with(mtcars, seq(min(cyl), max(cyl), length = steps) )

hp <- with(mtcars, seq(min(hp), max(hp), length = steps) )
newdat <- expand.grid(cyl = cyl, hp = hp)
carb <- matrix(predict(fit, newdat), steps, steps)

# Now plot it
p <- persp(cyl, hp, carb, theta = 45, col = "yellow")

# To add the points, you need the same 3d transformation
obs <- with(mtcars, trans3d(cyl, hp, carb, p))
pred <- with(mtcars, trans3d(cyl, hp, fitted(fit), p))
points(obs, col = "red", pch = 16)

# Add segments to show where the points are in 3d
segments(obs$x, obs$y, pred$x, pred$y)


That produces the following plot:



screen shot



You might not want to make predictions so far from the observed data. You can put NA values into carb to avoid that. This code does that:



exclude <- exclude.too.far(rep(cyl,steps), 
rep(hp, rep(steps, steps)),
mtcars$cyl,
mtcars$hp, 0.15) # 0.15 chosen by trial and error
carb[exclude] <- NA
p <- persp(cyl, hp, carb, theta = 45, col = "yellow")
obs <- with(mtcars, trans3d(cyl, hp, carb, p))
pred <- with(mtcars, trans3d(cyl, hp, fitted(fit), p))
points(obs, col = "red", pch = 16)
segments(obs$x, obs$y, pred$x, pred$y)


That produces this plot:



screen shot



Finally, you might want to use the rgl package to get a dynamic graph instead. After the same manipulations as above, use this code to do the plotting:



library(rgl)
persp3d(cyl, hp, carb, col="yellow", polygon_offset = 1)
surface3d(cyl, hp, carb, front = "lines", back = "lines")
with(mtcars, points3d(cyl, hp, carb, col = "red"))
with(mtcars, segments3d(rep(cyl, each = 2),
rep(hp, each = 2),
as.numeric(rbind(fitted(fit),
carb))))


Here's one possible view:



screen shot



You can use the mouse to rotate this one if you want to see it from a different angle. One other advantage is that points that should be hidden by the surface really are hidden; in persp, they'll plot on top even if they should be behind it.






share|improve this answer























  • Absolutely fantastic answer. You made my day. Thank you so much

    – Angelo
    yesterday















2














As @李哲源 pointed out in the comments, you shouldn't use plot here, because it's not flexible enough. Here's a version based on the referenced question Rough thin-plate spline fitting (thin-plate spline interpolation) in R with mgcv.



# First, get the fit
library(mgcv)
fit <- gam( carb ~ te(cyl, hp, k=c(3,4)), data = mtcars)

# Now expand it to a grid so that persp will work
steps <- 30
cyl <- with(mtcars, seq(min(cyl), max(cyl), length = steps) )

hp <- with(mtcars, seq(min(hp), max(hp), length = steps) )
newdat <- expand.grid(cyl = cyl, hp = hp)
carb <- matrix(predict(fit, newdat), steps, steps)

# Now plot it
p <- persp(cyl, hp, carb, theta = 45, col = "yellow")

# To add the points, you need the same 3d transformation
obs <- with(mtcars, trans3d(cyl, hp, carb, p))
pred <- with(mtcars, trans3d(cyl, hp, fitted(fit), p))
points(obs, col = "red", pch = 16)

# Add segments to show where the points are in 3d
segments(obs$x, obs$y, pred$x, pred$y)


That produces the following plot:



screen shot



You might not want to make predictions so far from the observed data. You can put NA values into carb to avoid that. This code does that:



exclude <- exclude.too.far(rep(cyl,steps), 
rep(hp, rep(steps, steps)),
mtcars$cyl,
mtcars$hp, 0.15) # 0.15 chosen by trial and error
carb[exclude] <- NA
p <- persp(cyl, hp, carb, theta = 45, col = "yellow")
obs <- with(mtcars, trans3d(cyl, hp, carb, p))
pred <- with(mtcars, trans3d(cyl, hp, fitted(fit), p))
points(obs, col = "red", pch = 16)
segments(obs$x, obs$y, pred$x, pred$y)


That produces this plot:



screen shot



Finally, you might want to use the rgl package to get a dynamic graph instead. After the same manipulations as above, use this code to do the plotting:



library(rgl)
persp3d(cyl, hp, carb, col="yellow", polygon_offset = 1)
surface3d(cyl, hp, carb, front = "lines", back = "lines")
with(mtcars, points3d(cyl, hp, carb, col = "red"))
with(mtcars, segments3d(rep(cyl, each = 2),
rep(hp, each = 2),
as.numeric(rbind(fitted(fit),
carb))))


Here's one possible view:



screen shot



You can use the mouse to rotate this one if you want to see it from a different angle. One other advantage is that points that should be hidden by the surface really are hidden; in persp, they'll plot on top even if they should be behind it.






share|improve this answer























  • Absolutely fantastic answer. You made my day. Thank you so much

    – Angelo
    yesterday













2












2








2







As @李哲源 pointed out in the comments, you shouldn't use plot here, because it's not flexible enough. Here's a version based on the referenced question Rough thin-plate spline fitting (thin-plate spline interpolation) in R with mgcv.



# First, get the fit
library(mgcv)
fit <- gam( carb ~ te(cyl, hp, k=c(3,4)), data = mtcars)

# Now expand it to a grid so that persp will work
steps <- 30
cyl <- with(mtcars, seq(min(cyl), max(cyl), length = steps) )

hp <- with(mtcars, seq(min(hp), max(hp), length = steps) )
newdat <- expand.grid(cyl = cyl, hp = hp)
carb <- matrix(predict(fit, newdat), steps, steps)

# Now plot it
p <- persp(cyl, hp, carb, theta = 45, col = "yellow")

# To add the points, you need the same 3d transformation
obs <- with(mtcars, trans3d(cyl, hp, carb, p))
pred <- with(mtcars, trans3d(cyl, hp, fitted(fit), p))
points(obs, col = "red", pch = 16)

# Add segments to show where the points are in 3d
segments(obs$x, obs$y, pred$x, pred$y)


That produces the following plot:



screen shot



You might not want to make predictions so far from the observed data. You can put NA values into carb to avoid that. This code does that:



exclude <- exclude.too.far(rep(cyl,steps), 
rep(hp, rep(steps, steps)),
mtcars$cyl,
mtcars$hp, 0.15) # 0.15 chosen by trial and error
carb[exclude] <- NA
p <- persp(cyl, hp, carb, theta = 45, col = "yellow")
obs <- with(mtcars, trans3d(cyl, hp, carb, p))
pred <- with(mtcars, trans3d(cyl, hp, fitted(fit), p))
points(obs, col = "red", pch = 16)
segments(obs$x, obs$y, pred$x, pred$y)


That produces this plot:



screen shot



Finally, you might want to use the rgl package to get a dynamic graph instead. After the same manipulations as above, use this code to do the plotting:



library(rgl)
persp3d(cyl, hp, carb, col="yellow", polygon_offset = 1)
surface3d(cyl, hp, carb, front = "lines", back = "lines")
with(mtcars, points3d(cyl, hp, carb, col = "red"))
with(mtcars, segments3d(rep(cyl, each = 2),
rep(hp, each = 2),
as.numeric(rbind(fitted(fit),
carb))))


Here's one possible view:



screen shot



You can use the mouse to rotate this one if you want to see it from a different angle. One other advantage is that points that should be hidden by the surface really are hidden; in persp, they'll plot on top even if they should be behind it.






share|improve this answer













As @李哲源 pointed out in the comments, you shouldn't use plot here, because it's not flexible enough. Here's a version based on the referenced question Rough thin-plate spline fitting (thin-plate spline interpolation) in R with mgcv.



# First, get the fit
library(mgcv)
fit <- gam( carb ~ te(cyl, hp, k=c(3,4)), data = mtcars)

# Now expand it to a grid so that persp will work
steps <- 30
cyl <- with(mtcars, seq(min(cyl), max(cyl), length = steps) )

hp <- with(mtcars, seq(min(hp), max(hp), length = steps) )
newdat <- expand.grid(cyl = cyl, hp = hp)
carb <- matrix(predict(fit, newdat), steps, steps)

# Now plot it
p <- persp(cyl, hp, carb, theta = 45, col = "yellow")

# To add the points, you need the same 3d transformation
obs <- with(mtcars, trans3d(cyl, hp, carb, p))
pred <- with(mtcars, trans3d(cyl, hp, fitted(fit), p))
points(obs, col = "red", pch = 16)

# Add segments to show where the points are in 3d
segments(obs$x, obs$y, pred$x, pred$y)


That produces the following plot:



screen shot



You might not want to make predictions so far from the observed data. You can put NA values into carb to avoid that. This code does that:



exclude <- exclude.too.far(rep(cyl,steps), 
rep(hp, rep(steps, steps)),
mtcars$cyl,
mtcars$hp, 0.15) # 0.15 chosen by trial and error
carb[exclude] <- NA
p <- persp(cyl, hp, carb, theta = 45, col = "yellow")
obs <- with(mtcars, trans3d(cyl, hp, carb, p))
pred <- with(mtcars, trans3d(cyl, hp, fitted(fit), p))
points(obs, col = "red", pch = 16)
segments(obs$x, obs$y, pred$x, pred$y)


That produces this plot:



screen shot



Finally, you might want to use the rgl package to get a dynamic graph instead. After the same manipulations as above, use this code to do the plotting:



library(rgl)
persp3d(cyl, hp, carb, col="yellow", polygon_offset = 1)
surface3d(cyl, hp, carb, front = "lines", back = "lines")
with(mtcars, points3d(cyl, hp, carb, col = "red"))
with(mtcars, segments3d(rep(cyl, each = 2),
rep(hp, each = 2),
as.numeric(rbind(fitted(fit),
carb))))


Here's one possible view:



screen shot



You can use the mouse to rotate this one if you want to see it from a different angle. One other advantage is that points that should be hidden by the surface really are hidden; in persp, they'll plot on top even if they should be behind it.







share|improve this answer












share|improve this answer



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answered Mar 7 at 18:34









user2554330user2554330

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  • Absolutely fantastic answer. You made my day. Thank you so much

    – Angelo
    yesterday

















  • Absolutely fantastic answer. You made my day. Thank you so much

    – Angelo
    yesterday
















Absolutely fantastic answer. You made my day. Thank you so much

– Angelo
yesterday





Absolutely fantastic answer. You made my day. Thank you so much

– Angelo
yesterday



















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