Plotting 3D Network

Question

I have a series of points that exist in 3 dimensional space (x, y, and z) and an adjacency matrix that determines connections between those points (see example below). How would I plot that? Thanks!

points  = matrix(c(2,3,2, 5,4,9, 4,1,8), byrow = TRUE, ncol = 3) #each row is a point and the colums are x, y, and z respectively
adj_mat = matrix(c(0,1,0, 1,0,1, 0,1,0), byrow = TRUE, ncol = 3)

Answer 1

There may be a more elegant way to handle the adjacency matrix, but as far as I can tell rgl::segments3d() turns sequential points into segments, so you need to repeat points for each connection. The below approach is slightly redundant; set the upper or lower triangle to 0 if you like, but you won't be able to see the difference anyway since the segments will overplot.

points  = matrix(
    c(2,3,2, 5,4,9, 4,1,8), 
    byrow = TRUE, ncol = 3, 
    dimnames = list(NULL, c('x', 'y', 'z'))
)
adj_mat = matrix(c(0,1,0, 1,0,1, 0,1,0), byrow = TRUE, ncol = 3)


segments <- points[as.vector(matrix(
    c(row(points)[as.logical(adj_mat)], 
      col(points)[as.logical(adj_mat)]), 
    byrow = TRUE, nrow = 2
)), ] 

library(rgl)

plot3d(points)
segments3d(segments)