3D Plotting in R

Question

I'm trying to create a 3D plot of a function, but the message "Error in persp.default(x = xseq, y = yseq, matrixz, phi = -5, theta = 50, : incorrect z limits" appears. I have no idea why

yseq <- seq(1e-9,1e-7,by=1e-9)
xseq <- seq(1e-8,1e-4,by=1e-6)
matrixz <- matrix(data = 0,nrow=length(xseq),ncol=length(yseq))

persp(x=xseq,y=yseq, matrixz, phi=-5, theta=50, expand=0.5, col="red4",xlab="[Ca] cytosol",ylab="[InsP3]",zlab="J2(x,y)", ticktype="detailed")

Any help would be greatly appreciated !

Answer 1

Well, the matrixz is only filled with 0s and the range of it, does not please persp and explains your error message:

> range(matrixz)
[1] 0 0

You can fix this by defining a zlim :

yseq <- seq(1e-9, 1e-7, by=1e-9)
xseq <- seq(1e-8, 1e-4, by=1e-6)
matrixz <- matrix(data =0, nrow=length(xseq), ncol=length(yseq))

persp(xseq, yseq, matrixz, phi=-5, zlim=c(-1e-3, 1e-3), 
      theta=50, expand=0.5, col="red4",xlab="[Ca] cytosol",ylab="[InsP3]",zlab="J2(x,y)", 
      ticktype="detailed")

or by filling your matrix, with your data. Here we sample numbers from the uniform distribution:

matrixz <- matrix(data = runif(length(xseq)*length(yseq)), nrow=length(xseq), ncol=length(yseq))

persp(xseq, yseq, matrixz, phi=-5, theta=50, expand=0.5,    
      col="red4",xlab="[Ca] cytosol",ylab="[InsP3]",zlab="J2(x,y)",  
      ticktype="detailed")

If you don't want to bother with a particular theta , phi , etc. you can explore your 3D plot with persp3d from rgl :

library(rgl)
persp3d(xseq, yseq, matrixz)