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UCLouvain-CBIO / scp

Single cell proteomics data processing
https://uclouvain-cbio.github.io/scp/index.html
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Help to replicate graph #47

Closed prvst closed 8 months ago

prvst commented 8 months ago

Hello, could you please show me how to replicate Figures 8, and 9 from this https://arxiv.org/abs/2310.13598?

Thanks

lgatto commented 8 months ago

Not sure it's available in the Rmd file on the zenodo archive (10.5281/zenodo.8417228), but it's a rather standard type of plot that can be generated with data in a QFeatures object. There's a similar figure in section 5.4.9 (figure 5/14) in the Quantitative data chapter of the R4MS book.

Would this address your question?

prvst commented 8 months ago

Yes, that helps. I was trying to figure it out how to pull data from the different layers (PSM, peptides, and protein) into one data frame.

Thanks, Laurent

Also, nice job with the publication above, good to see people working with open and clear methods that make sense, for single-cell.

Cheers,