I have some gene expression data from various tissue types. I first wanted to use R to make a UMAP, and followed this wonderful and simple tutorial on how to do so using the
Here's my result:
My challenge is, however, that I've been asked to optimize this plot such that there is a maximum separation of the tissue types. In other words - is there any parameter than can be tweaked such that other tissue types can be further separated/clustered for maximum isolation?
My issue is that I can tweak
umapr's parameters like number of neighbors, number of components, number of training epochs, learning rate, etc etc....but testing all the combinations would take me until the end of time. This is an example of just tweaking two options, but there are millions of possible combinations when considering all paramters.