Hi,
Welcome to the RStudio community!
Could you please explain what the end result is supposed to look like. I don't understand the 3D part as you said you want to create 41 heatmaps and use the heatmap1 function although there is a profileplot3d function in that package as well, which does look confusion I must say.
I also suggest you read how to create a reprex, as your code now is very confusing. A reprex consists of the minimal code and data needed to recreate the issue/question you're having. You can find instructions how to build and share one here:
I don't think this is what you want, but here is some code I wrote based on your question:
library(NeatMap)
#Generate a dummy matrix
m1 = matrix(1:(41*2500*41), nrow=41*2500, ncol=41)
#Split into 41 matrices of each 2500 rows
m1 = lapply(1:41, function(x){
m1[(1+2500*(x-1)):(2500*x),]
})
#Generate a heatmap for every of the 41 matrices
heatmaps = lapply(m1, heatmap1)
#Render a heatmap
heatmaps[[1]]
Please elaborate and update the code, and we can work from there.
Hope this helps,
PJ