Question: How can I replicate the t-SNE plot in Loupe Cell Browser?
Answer: The t-SNE plot in Loupe Cell Browser is based on the secondary analysis generated by Cell Ranger.
The underlying data for the t-SNE plot are in one of the Cell Ranger output files.
$ head -5 analysis/tsne/2_components/projection.csv
Barcode,TSNE-1,TSNE-2
AAACATACAACGAA-1,-13.5494,1.4674
AAACATACTACGCA-1,-2.7325,-10.6347
AAACCGTGTCTCGC-1,12.9590,-1.6369
AAACGCACAACCAC-1,-9.3585,-6.7300
The t-SNE algorithm is described here within the "Dimensionality Reduction" section. The t-SNE parameters used in cellranger count are listed here as default parameters in cellranger reanalyze. The t-SNE-specific parameters have the prefix "tsne_".
Here is the section of code for running t-SNE in the last open-source release of Cell Ranger.