settings for scJoint

[Desi0]

Hi,

I am wondering, can somebody help me with choosing the settings in config.py ?
I have integrated scRNA-Seq data with several differing factors (different technologies, stim and ctrl, different Age). I also have scATAC data, but from a completely different batch of samples.
After running scJoint according to the 10X tutorial notebook, the two datasets do not look nicely overlayed in the tSNE-plot.
Is there maybe a possibility to use pre-calculated embedding-values for RNA, so that the clustering/plotting is the same as in Seurat and the ATAC cells will be put in this embedding?
Or can I change the resolution of the tSNE somehow?

As I am a newby to python and this kind of analysis, I'd appreciate any help.

Thanks!