So I've decided to write a program to compute dimension reduction and potentially clustering specifically for single cell RNAseq. I got tired of running PCA/t-SNE in R, where I do most of my downstream analysis, since t-SNE specifically takes such a long time to run. Typically I'll run t-SNE with several different perplexity values to see which visualizations I like best; this is computationally intensive. I know that C++ and Python are both significantly faster than R; my question is, if I wanted to write this program in either of those languages and then call it from R, using either
reticulate, which should I use if my main aim is speed? I'm confident in my ability to write the code in either language, but I'd rather not do it twice, and I'm not familiar with the speed / ease of integration of either of those two packages.