Unable to see gene expression in SPRING viewer

[Alice Lam]

Hi!

I followed the spring_example_pmbc_4k example as well as the cell labeling with SignacX using my own data, and was able to generate a SPRING plot that looks like what I would have expected based on other clustering packages. However, when I try to look at expression by gene, nothing shows up despite the expression scalebar changing depending on what gene is entered. Similarly, I do not get a list of enriched genes when I select a group of cells from the cell labels. For instance, this is the output for two genes in my dataset showing the different scale bars:


and this is the empty gene list for a group of selected cells:

Do you have any suggestions as to what to do from here?

[Caleb Weinreb]

Hi!

First, can you confirm that you started a CGI server locally to launch the viewer? Are there any error messages reported in the terminal where you launched the server?

Is that's not the issue, then the easiest thing would be send me a copy of the spring project that was generated ([e-mail])

[Alice Lam]

Hi!

Thanks for the suggestions! I had started a CGI server locally but didn't realize my conda env had python3 activated. I switched to python2 and have now resolved the problem.