Plot 3D data in R

Question

I have a 3D dataset   data   data frame      x   rep  c 0 1  0 2  0 3  0 4  0 5   each 5       y   rep  c 1  2  3  4  5   5     data z   runif      25      min    data x data y - 0 1    data x data y        max    data x data y   0 1    data x data y      data str data    And I want to plot it  but the built-in-functions of R alwyas give the error      increasing  x  and  y  values expected         3D Plots                                                          built-in function always give the error       increasing  x  and  y  values expected  demo image  image x   data x  y   data y  z   data z   demo persp  persp data x data y data z   contour data x data y data z    When I searched on the internet  I found that this message happens when combinations of X and Y values are not unique  But here they are unique   I tried some other libraries and there it works without problems  But I don t like the default style of the plots  the built-in functions should fulfill my expectations          3D Scatterplot                                                          Nice plots without surface maps  install packages  scatterplot3d   dependencies   TRUE  library scatterplot3d  scatterplot3d x   data x  y   data y  z   data z         3D Scatterplot                                                          Only to play around  install packages  rgl   dependencies   TRUE  library rgl  plot3d x   data x  y   data y  z   data z  lines3d x   data x  y   data y  z   data z  surface3d x   data x  y   data y  z   data z    Why are my datasets not accepted by the built-in functions

User · Accepted Answer

If you re working with  real  data for which the grid intervals and sequence cannot be guaranteed to be increasing or unique  hopefully the  x y z  combinations are unique at least  even if these triples are duplicated   I would recommend the akima package for interpolating from an irregular grid to a regular one    Using your definition of data   library akima  im  lt - with data interp x y z   with im image x y z       And this should work not only with image but similar functions as well   Note that the default grid to which your data is mapped to by akima  interp is defined by 40 equal intervals spanning the range of x and y values    gt  formals akima  interp  c  xo   yo     xo seq min x   max x   length   40    yo seq min y   max y   length   40    But of course  this can be overridden by passing arguments xo and yo to akima  interp

User · Answer

I think the following code is close to what you want  x     lt - c 0 1  0 2  0 3  0 4  0 5  y     lt - c 1  2  3  4  5  zfun  lt - function a b   a b     0 9   0 2 runif a b     z     lt - outer x  y  FUN  zfun     It gives data like this  note that x and y are both increasing    gt  x  1  0 1 0 2 0 3 0 4 0 5  gt  y  1  1 2 3 4 5  gt  z             1         2         3         4         5   1   0 1037159 0 2123455 0 3244514 0 4106079 0 4777380  2   0 2144338 0 4109414 0 5586709 0 7623481 0 9683732  3   0 3138063 0 6015035 0 8308649 1 2713930 1 5498939  4   0 4023375 0 8500672 1 3052275 1 4541517 1 9398106  5   0 5146506 1 0295172 1 5257186 2 1753611 2 5046223   and a graph like  persp x  y  z

User · Answer

Adding to the solutions of others  I d like to suggest using the plotly package for R  as this has worked well for me   Below  I m using the reformatted dataset suggested above  from xyz-tripplets to axis vectors x and y and a matrix z   x  lt - 1 5 10 y  lt - 1 5 z  lt - x  o  y z  lt - z    2 z runif 25  -  1 z  library plotly  plot ly x x y y z z  type  surface       The rendered surface can be rotated and scaled using the mouse  This works fairly well in RStudio   You can also try it with the built-in volcano dataset from R   plot ly z volcano  type  surface

User · Answer

I use the lattice package for almost everything I plot in R and it has a corresponing plot to persp called wireframe  Let data be the way Sven defined it   wireframe z   x   y  data data      Or how about this  modification of fig 6 3 in Deepanyan Sarkar s book    p  lt - wireframe z   x   y  data data  npanel  lt - c 4  2  rotx  lt - c -50  -80  rotz  lt - seq 30  300  length   npanel 1  1  update p rep 1  prod npanel     layout   npanel      panel   function      screen            panel wireframe      screen   list z   rotz current column                                                x   rotx current row                 Update  Plotting surfaces with OpenGL  Since this post continues to draw attention I want to add the OpenGL way to make 3-d plots too  as suggested by  tucson below   First we need to reformat the dataset from xyz-tripplets to axis vectors x and y and a matrix z   x  lt - 1 5 10 y  lt - 1 5 z  lt - x  o  y z  lt - z    2 z runif 25  -  1 z  library rgl  persp3d x  y  z  col  skyblue       This image can be freely rotated and scaled using the mouse  or modified with additional commands  and when you are happy with it you save it using rgl snapshot   rgl snapshot  myplot png

User · Answer

Not sure why the code above did not work for the library rgl  but the following link has a great example with the same library  Run the code in R and you will obtain a beautiful 3d plot that you can turn around in all angles   http   statisticsr blogspot de 2008 10 some-r-functions html                                                                              another example of 3d plot from my personal reserach  use rgl library                                                                            3D visualization device system  library rgl   data volcano  dim volcano   peak height  lt - volcano  ppm index  lt -  1 nrow volcano    sample index  lt -  1 ncol volcano     zlim  lt - range peak height  zlen  lt - zlim 2  - zlim 1    1 colorlut  lt - terrain colors zlen    height color lookup table col  lt - colorlut  peak height-zlim 1  1     assign colors to heights for each point open3d    ppm index1  lt - ppm index zlim 2  max ppm index   sample index1  lt - sample index zlim 2  max sample index   title name  lt - paste  plot3d     volcano   sep        surface3d ppm index1  sample index1  peak height  color col  back  lines   main   title name   grid3d c  x    y     z    n  20   sample name  lt - paste  col    1 ncol volcano   sep      sample label  lt - as integer seq 1  length sample name   length   5     axis3d  y   at   sample index1 sample label   sample name sample label   cex   0 3   axis3d  y  at   sample index1 sample label   sample name sample label   cex   0 3  axis3d  z  pos c 0  0  NA    ppm label  lt - as integer seq 1  length ppm index   length   10    axes3d  x   at c ppm index1 ppm label   0  0   abs round ppm index ppm label   2    cex   0 3    title3d main   title name  sub    test   xlab    ppm   ylab    samples   zlab    peak   rgl bringtotop

[r] Plot 3D data in R

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