ypriverol
commented
2 years ago Dear @Douerww :
Thanks a lot for your hard work. The tools look amazing now. I have tested it, and it works better than before.
Importing data:
- [x] Would be great if we can import .csv and .csv.gz (This will help users to upload small files)
- [x] I have cleaned the project, but I found that the application shiny is in here pquant and in docker/pquantr we should have only one path.
- [x] The dynamic plot doesn't work for me. It asks me to annotate manually the mzML files related with conditions. I don't know why this is needed, you know the
factor value[?] -> conditionfor each mzML in the msststats output. - [x] Change all the references to proteomicLFQ to quantms. Because in the future they will be only one pipeline for quantitation quantms containing TMT and LFQ data.
- [x] Protein accessions are to big in some cases, what do you think about having a logic that transform accessions from:
- [ ] Long Uniprot Accession -> ProteinID
- [ ] Long Uniprot Accession -> Gene Accession
@Douerww Some major improvements we should do:
Can we remove the heatmap generation using python an use R. I think we should remove the python call from the code.
I guess the plot instead of one close to another should be one after another.
I think we should try to avoid this https://github.com/bigbio/pquant/blob/7de59460cc7a57ce80797cc947c84a8f9457f67a/pquant/shiny-app/app.R#L264 Why if the user provide a file, we need to go to data, should'nt be possible to read from what ever user give you. One solution would be to copy the file to the sample where the application is stored.
When the user select a protein in the protein table, it should be possible to change the panels in the protein plots. I think that was the approach of Proteus shiny.