Actually, I found one weird behavior after I made the above change. Whenever I applied plotTSNE() to my updated object, the location of clusters in the plot changes with different 'colour_by' argument. I have no idea why this is happening. Any advice to resolve this?

You're going to have to be more specific about the code that you actually ran. I'm guessing that you re-ran plotTSNE on the sce object that did not already contain precomputed t-SNE coordinates. This recomputes the t-SNE coordinates so if you don't set the random seed, you'll get different coordinates for all points. So, you can either:

1. Set the seed prior to each plotTSNE call. This is the simplest solution.
2. Precompute t-SNE coordinates and store them in the sce object using runTSNE. Then, all ensuing plotTSNE calls will use the precomputed coordinates rather than recomputing it at every call. This is the preferred solution for experienced users as it avoids wasting time in redundant calculations when all you want to do is to change the colour of the points (or various other aesthetics that have nothing to do with the t-SNE itself).

Previous versions of scater set the seed internally for convenience. However, this was probably a Bad Idea because it silently changes the behaviour of all downstream functions that depend on randomization - see the commentary at WARNING: remove set.seed usage in R code. As such, this behaviour was deprecated in the last release and removed in this release.