tSNE Clustering Thresholds

[AAA-3]

Hello everyone,

This is not an issue with the program but rather a discussion topic to help me understand the following:

The vignette has a section in Part A which dimensionally reduced the LDA distributions into a tsne with two optionss (runtSNE and Rtsne).

This is followed by creating a graph to check thresholds. I want to know if:

1. What are these thresholds for?
2. Why are the red clusters important?

[cbravo93]

This is the density peak clustering algorithm used by Monocle 2 as in: https://www.nature.com/articles/nature25981#Sec2 . You can find more information in the Monocle 2 paper: https://www.nature.com/articles/nmeth.4402 and in the original algorithm paper: https://www.science.org/doi/10.1126/science.1242072

Cheers!

C