R Plotting a 3D surface from x y z

Question

imagine I have a 3 columns matrix x  y  z where z is a function of x and y   I know how to plot a  scatter plot  of these points with plot3d x y z   But if I want a surface instead I must use other commands such as  surface3d  The problem is that it doesn t accept the same inputs as plot3d it seems to need a matrix with    n   elements of z     n of elements of x     n of elements of x    How can I get this matrix  I ve tried with the command interp  as I do when I need to use contour plots   How can I plot a surface directly from x y z without calculating this matrix  If I had too many points this matrix would be too big   cheers

User · Answer

You could look at using Lattice   In this example I have defined a grid over which I want to plot z x y   It looks something like this   Note that most of the code is just building a 3D shape that I plot using the wireframe function   The variables  b  and  s  could be x or y   require lattice     begin generating my 3D shape b  lt - seq from 0  to 20 by 0 5  s  lt - seq from 0  to 20 by 0 5  payoff  lt - expand grid b b s s  payoff payoff  lt - payoff b - payoff s payoff payoff payoff payoff  lt  -1   lt - -1   end generating my 3D shape   wireframe payoff   s   b  payoff  shade   TRUE  aspect   c 1  1       light source   c 10 10 10   main    Study 1       scales   list z ticks 5 arrows FALSE  col  black   font 10  tck 0 5       screen   list z   40  x   -75  y   0

User · Answer

Maybe is late now but following Spacedman  did you try duplicate  strip  or any other option   x runif 1000  y runif 1000  z rnorm 1000  s interp x y z duplicate  strip   surface3d s x s y s z color  blue   points3d s

User · Answer

You can use the function outer   to generate it    Have a look at the demo for the function persp    which is a base graphics function to draw perspective plots for surfaces    Here is their first example   x  lt - seq -10  10  length out   50    y  lt - x   rotsinc  lt - function x y        sinc  lt - function x    y  lt - sin x  x   y is na y    lt - 1  y         10   sinc  sqrt x 2 y 2         z  lt - outer x  y  rotsinc    persp x  y  z    The same applies to surface3d     require rgl    surface3d x  y  z

User · Answer

rgl is great  but takes a bit of experimentation to get the axes right     If you have a lot of points  why not take a random sample from them  and then plot the resulting surface    You can add several surfaces all based on samples from the same data to see if the process of sampling is horribly affecting your data     So  here is a pretty horrible function but it does what I think you want it to do  but without the sampling    Given a matrix  x  y  z  where z is the heights it will plot both the points and also a surface   Limitations are that there can only be one z for each  x y  pair   So planes which loop back over themselves will cause problems   The plot points   T will plot the individual points from which the surface is made - this is useful to check that the surface and the points actually meet up  The plot contour   T will plot a 2d contour plot below the 3d visualization   Set colour to rainbow to give pretty colours  anything else will set it to grey  but then you can alter the function to give a custom palette   This does the trick for me anyway  but I m sure that it can be tidied up and optimized   The verbose   T prints out a lot of output which I use to debug the function as and when it breaks     plot rgl model a  lt - function fdata  plot contour   T  plot points   T                                verbose   F  colour    rainbow   smoother   F        takes a model in long form  in the format      1st column x      2nd is y       3rd is z  height       and draws an rgl model       includes a contour plot below and plots the points in blue      if these are set to TRUE      note that x has to be ascending  followed by y   if  verbose  print head fdata      fdata  lt - fdata order fdata   1   fdata   2        if  verbose  print head fdata          require reshape2    require rgl    orig names  lt - colnames fdata    colnames fdata   lt - c  x    y    z     fdata  lt - as data frame fdata        work out the min and max of x y z   xlimits  lt - c min fdata x  na rm   T   max fdata x  na rm   T     ylimits  lt - c min fdata y  na rm   T   max fdata y  na rm   T     zlimits  lt - c min fdata z  na rm   T   max fdata z  na rm   T     l  lt - list  x   xlimits  y   ylimits  z   zlimits    xyz  lt - do call expand grid  l    if  verbose  print xyz    x boundaries  lt - xyz x   if  verbose  print class xyz x     y boundaries  lt - xyz y   if  verbose  print class xyz y     z boundaries  lt - xyz z   if  verbose  print class xyz z     if  verbose  print paste x boundaries  y boundaries  z boundaries  sep              now turn fdata into a wide format for use with the rgl surface   fdata   2   lt - as character fdata   2     fdata   3   lt - as character fdata   3      if  verbose  print class fdata   2      wide form  lt - dcast fdata  y   x  value var    z     if  verbose  print head wide form     wide form values  lt - as matrix wide form   2 ncol wide form        if  verbose  print wide form values    x values  lt - as numeric colnames wide form 2 ncol wide form       y values  lt - as numeric wide form   1     if  verbose  print x values    if  verbose  print y values    wide form values  lt - wide form values order y values   order x values     wide form values  lt - as numeric wide form values    x values  lt - x values order x values     y values  lt - y values order y values     if  verbose  print x values    if  verbose  print y values     if  verbose  print dim wide form values     if  verbose  print length x values     if  verbose  print length y values      zlim  lt - range wide form values    if  verbose  print zlim    zlen  lt - zlim 2  - zlim 1    1   if  verbose  print zlen     if  colour     rainbow        colourut  lt - rainbow zlen  alpha   0      if  verbose  print colourut      col  lt - colourut  wide form values - zlim 1    1        if  verbose  print col      else       col  lt -  grey      if  verbose  print table col2           open3d     plot3d x boundaries  y boundaries  z boundaries            box   T  col    black    xlab   orig names 1             ylab   orig names 2   zlab   orig names 3      rgl surface z   x values      these are all different because               x   y values      of the confusing way that                y   wide form values      rgl surface works  - y is the height                coords   c 2 3 1                 color   col                alpha   1 0                lit   F                smooth   smoother     if  plot points         plot points in red just to be on the safe side      points3d fdata  col    blue          if  plot contour         plot the plane underneath     flat matrix  lt - wide form values     if  verbose  print flat matrix      y intercept  lt -  zlim 2  - zlim 1      -2 3    put the flat matrix 1 2 the distance below the lower height      flat matrix which flat matrix    y intercept    lt - y intercept     if  verbose  print flat matrix       rgl surface z   x values      these are all different because                 x   y values      of the confusing way that                  y   flat matrix      rgl surface works  - y is the height                  coords   c 2 3 1                   color   col                  alpha   1 0                  smooth   smoother          The add rgl model does the same job without the options  but overlays a surface onto the existing 3dplot     add rgl model  lt - function fdata         takes a model in long form  in the format      1st column x      2nd is y       3rd is z  height       and draws an rgl model           note that x has to be ascending  followed by y   print head fdata      fdata  lt - fdata order fdata   1   fdata   2         print head fdata          require reshape2    require rgl    orig names  lt - colnames fdata      print head fdata     colnames fdata   lt - c  x    y    z     fdata  lt - as data frame fdata        work out the min and max of x y z   xlimits  lt - c min fdata x  na rm   T   max fdata x  na rm   T     ylimits  lt - c min fdata y  na rm   T   max fdata y  na rm   T     zlimits  lt - c min fdata z  na rm   T   max fdata z  na rm   T     l  lt - list  x   xlimits  y   ylimits  z   zlimits    xyz  lt - do call expand grid  l     print xyz    x boundaries  lt - xyz x    print class xyz x     y boundaries  lt - xyz y    print class xyz y     z boundaries  lt - xyz z    print class xyz z        now turn fdata into a wide format for use with the rgl surface   fdata   2   lt - as character fdata   2     fdata   3   lt - as character fdata   3      print class fdata   2      wide form  lt - dcast fdata  y   x  value var    z     print head wide form     wide form values  lt - as matrix wide form   2 ncol wide form        x values  lt - as numeric colnames wide form 2 ncol wide form       y values  lt - as numeric wide form   1     print x values    print y values    wide form values  lt - wide form values order y values   order x values     x values  lt - x values order x values     y values  lt - y values order y values     print x values    print y values     print dim wide form values     print length x values     print length y values      rgl surface z   x values      these are all different because               x   y values      of the confusing way that                y   wide form values      rgl surface works                coords   c 2 3 1                 alpha    8      plot points in red just to be on the safe side    points3d fdata  col    red       So my approach would be to  try to do it with all your data  I easily plot surfaces generated from  15k points    If that doesn t work  take several smaller samples and plot them all at once using these functions

User · Answer

If your x and y coords are not on a grid then you need to interpolate your x y z surface onto one  You can do this with kriging using any of the geostatistics packages  geoR  gstat  others  or simpler techniques such as inverse distance weighting   I m guessing the  interp  function you mention is from the akima package  Note that the output matrix is independent of the size of your input points  You could have 10000 points in your input and interpolate that onto a 10x10 grid if you wanted  By default akima  interp does it onto a 40x40 grid   require akima  require rgl   x   runif 1000  y   runif 1000  z   rnorm 1000  s   interp x y z   gt  dim s z   1  40 40 surface3d s x s y s z    That ll look spiky and rubbish because its random data  Hopefully your data isnt

[r] R: Plotting a 3D surface from x, y, z

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