Add tissue imperfections to R object + spatialLIBD app

[lcolladotor]

• [x] Get all the CSV files from Kristen's manual annotation of tissue imperfections (folds and the like)
• [x] Import them and put them together as a single CSV file (version control it here)
• [x] Update https://github.com/LieberInstitute/spatialDLPFC/blob/main/code/analysis/01_build_spe/03_add_deconvolution.R
• [x] Re-deploy the spatialLIBD apps

[lcolladotor]

Prashanti @prashanthi-ravichandran,

I talked with Nick @Nick-Eagles and he can help you a bit with this. Ideally, I want the SPE object that we'll share to have all the info on it.

Though well, I know that maybe we are dropping some tissue artifact spots along the way (like in the low library size filtering step), so they might not be on the final SPE. In any case, the repo should contain the CSV files with all the tissue artifact labels. Having the final SPE object contain the manually label artifacts will also be useful regardless if it's a subset.

We can talk more about this on Thursday.

[lcolladotor]

Do you have any updates on this @Nick-Eagles?

[Nick-Eagles]

I wrote working code to add the wrinkle and layer annotation to the SPE object here, and I'll aim to integrate/ move this code to your shiny deployment script as we discussed by the end of today. Are you still interested in putting the CSVs together as one CSV (my current code handles the files separately as I received them)?

[lcolladotor]

We don't need to put the CSVs together into one file. It's ok to have multiple ones. We do want to have a single R object though

[Nick-Eagles]

I updated (but did not fully run) the R script, which will add the colData columns wrinkle_type and manual_layer_label. Let me know if I should run the script (and overwrite the session info at the bottom) or help out with the deployment.

[Nick-Eagles]

I now see your slack comment about updating the lobstr info and documenting the new variable names, so I'll run the script and do that.

[lcolladotor]

Thanks Nick! Yup, let me know once you are done re-making this SPE object, thanks!

[Nick-Eagles]

It's ready to deploy!

[lcolladotor]

Cool, thanks Nick!