How to plot a 3D surface of a 3D matrix with R

Question

I have 3D matrix of floating point numbers and I would like to produce a smoothed 3D surface of this matrix using R. Any suggestions are welcome. Thanks

Now I am using scatterplot3d ... But this function did not produce a smoothed surface

x<-read.table("/Users/me/Desktop/data.txt")
scatterplot3d(x$V1, x$V2, x$V3, highlight.3d = TRUE, angle = 30, col.axis = "blue", col.grid = "lightblue", cex.axis = 1.3, cex.lab = 1.1, pch = 20)

Outputting a portion of your data will greatly increase your chances of getting help. You can simply paste the output of `dput(head(x))` into your question above. Thanks — Simon O'Hanlon, Mar 07 '13 at 16:18
> dput(head(x)) structure(list(V1 = c(0.01, 0.013971025, 0.019832054, 0.021035526, 0.023956488, 0.027962379), V2 = c(0.01, 0.011738323, 0.011925891, 0.011990806, 0.013416452, 0.014304923), V3 = c(8.21e-19, 3.47e-17, 1.77e-15, 3.64e-15, 1.39e-14, 5.46e-14)), .Names = c("V1", "V2", "V3"), row.names = c(NA, 6L), class = "data.frame") — Mohamed Bouguessa, Mar 07 '13 at 16:28
Put the dput dump in the question! The idea here is improved improved questions and answers. — mdsumner, Mar 07 '13 at 19:40

score 2 · Answer 1 · answered Mar 07 '13 at 16:28

2

If you are able to create a 2D matrix (x,y) with the value being the z-axis value you could use the following

persp

Here is an example from R Graph Gallery. persp example

answered Mar 07 '13 at 16:28

larrydag

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score 2 · Answer 2 · answered Mar 07 '13 at 16:31

require(misc3d)

a <- 2/5

wsqr <-  1 - a^2
w <- sqrt(wsqr)
denom <- function(a,w,u,v) a*((w*cosh(a*u))^2 + (a*sin(w*v))^2)

fx <- function(u,v) -u + (2*wsqr*cosh(a*u)*sinh(a*u)/denom(a,w,u,v))
fy <- function(u,v) 2*w*cosh(a*u)*(-(w*cos(v)*cos(w*v)) - (sin(v)*sin(w*v)))/denom(a,w,u,v)
fz = function(u,v) 2*w*cosh(a*u)*(-(w*sin(v)*cos(w*v)) + (cos(v)*sin(w*v)))/denom(a,w,u,v)


parametric3d(fx = fx, fy = fy, fz = fz, 
             umin = -17, 
             umax = 17, 
             vmin = -77, 
             vmax = 77, 
             n = 100,
             color = c("grey17","grey21","red4","darkred","red4","grey21","grey17"),
             engine = "rgl")

enter image description here

score 2 · Accepted Answer · answered Mar 07 '13 at 16:47

I think that mba.surf from the MBA package would be a good choice for the smoothing, and as larrydag above suggests, persp would be good to image it. The code below is from the help page for the mba.surf function (swap LIDAR for your 3 column dataframe):

data(LIDAR)
mba.int <- mba.surf(LIDAR, 300, 300, extend=TRUE)$xyz.est
# Two ways of imaging....
image(mba.int, xaxs="r", yaxs="r")
persp(mba.int, theta = 135, phi = 30, col = "green3", scale = FALSE,
  ltheta = -120, shade = 0.75, expand = 10, border = NA, box = FALSE)

enter image description here

How to plot a 3D surface of a 3D matrix with R

3 Answers3