The 3rd hypercube is the cube below where planes cover the space in different ways. The 4th hypercube can be considered as many connected 3rd hypercubes. You are interested in planes, the example is from XRD lab related to solid state physics and crystallography.

Hosts such as ArXiv require certain TexLive version such as 2011 where you cannot use newer tools resulting into easy autogenerated pictures like here. You manually convert the pictures to images. For example in the case of TikZ you use \usetikzlibrary{external}\tikzexternalize and then use basic \includegraphics{...} as instructed by yo'. The manual conversion can ensure easier compiling of the future but an extra workflow step, taking time. You want to facilitate easy co-operation with your papers so people can adjust the sources for their research.
Which packages to visualise the planes in hypercubes?
Is it better to build the visualisation codes inside the LaTex document or separately compile the pictures each time when updates?
Is it better to rely on newer packages or older packages to avoid possible dependency problems of the future?
How would you visualise the planes in your recommended package? Is it easy to use that package for higher dimensional cubes? You can consider the higher dimensional cubes in terms of graphs with higher vertex order.
"as is"related to XRD lab and I have no clue how it was generated. I feel it may have been generated with some LaTex package such as TikZ, PSTricks and tkz-berge. I have no clue what the best technique is to proceed. – hhh Mar 22 '15 at 15:56miller. – Johannes_B Mar 22 '15 at 16:06