Micka&#235;l Perrier - 1 year ago 61
R Question

# How to 3D plot matrices that are not squared in R?

I would like to plot a heatmap using my own mathematical function instead of the Kernel density estimation. But for the moment my problem comes from the fact that I cannot 3D plot this function using

`persp()`
if my
`x`
&
`y`
axes are not squared. Indeed the heatmap is sized 855 x 670.

1) Is there a way to solve this problem?

2) Plus, does anyone know how to turn this into a heatmap?

Thanks in advance. Please, find a part of my script below.

–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––

Here are two functions we will need:

``````rep.row <- function(x, n){
matrix(rep(x, each = n), nrow = n)
}
rep.col <- function(x, n){
matrix(rep(x, each = n), ncol = n, byrow = TRUE)
}
``````

This reads an image and extracts its dimensions (i.e., width and length):

``````require('png')
png <- readPNG("myImage.png")
res <- dim(png)[2:1]
``````

For information:

``````> dim(png)[2:1]
[1] 855 670
``````

These are fixed parameters:

``````alphaW <- 53
alphaH <- 31
a <- 2.3
``````

I create two vectors (i.e.,
`e1`
and
`e2`
) based on the image dimensions. Therefore,
`e1`
is 855-cells long and
`e2`
is 670-cells long. Then I use the functions above in order to create two matrices (i.e.,
`E1`
and
`E2`
) the same size of the image (i.e., 855 x 670).

``````e1 <- seq(-alphaW, alphaW, length = res[1])
e2 <- seq(-alphaH, alphaH, length = res[2])

E1 <- rep.row(e1, res[2])
E2 <- rep.col(e2, res[1])
``````

A computation of these two matrices is used to create a 3rd matrix,
`SV`
:

``````SV <- sqrt((a / (a + ((E1^2) + (E2^2)))))
``````

Finally I want to plot a 3D representation of this matrix:

``````persp(x = e1, y = e2, z = SV,
col = "lightgoldenrod",
border = NA,
theta = 30,
phi = 15,
ticktype = "detailed",
ltheta = -120,
shade = 0.25)
``````

This should output something like {this}, however, I receive:

``````Error in persp.default(e1, e2, SV, col = "lightgoldenrod", border = NA,  :
argument 'z' incorrect
``````

Answer Source

You switched x and y. If you look at the help page for persp(), you will notice that x should have length nrow(z) and y length ncol(z). So although intuitively you might expect rows to be on the vertical axis (how you visualise the matrix), it seems to be the other way around.

This works:

``````persp(y = e1, x = e2, z = SV,
col = "lightgoldenrod",
border = NA,
theta = 30,
phi = 15,
ticktype = "detailed",
ltheta = -120,
shade = 0.25)
``````
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