Update readMerscopeSXE.R

[drighelli]

"X" is not the only possible value for "cell" in metadata file for merfish data (if we want to make it adaptable also to it).

I also suggest to use the fread function to load metadata files (you already have an import on data.table).

Finally, you want to be sure that metadata$cell is a character, because you are going to assign it as rownames.

I'm trying to encapsulate your functions into SpaceTrooper functions and this fails when loading merfish data.

Would you consider to include this change into your function?

Thanks,
Dario

[estellad]

Hi Dario,

Thank you for the PR! I agree with the fread and as.character() modification.

About this line - names(metadata)[names(metadata) %in% c("EntityID", "V1", "X")] <- "cell", have you tested if it will cause conflict when merging?

Would it be possible that a metadata file contains all three columns named "EntityID", "V1", "X", and all of them will be renamed to "cell"? If we are certain that each metadata file can only contain one of the three, then I am fine with merge your PR.

Sincerely,
Estella

[drighelli]

Hi @estellad,

you are totally right, I cannot be absolutely sure about this, I can implement something different with a new commit.

[drighelli]

see the commit message for this new commit.

Let me know if this can work, otherwise I can think about something different.

[estellad]

Hi Dario,

I would update the else statement to names(metadata)[idxcell[1]] <- "cell", so we take the first one of many idxcell. As long as we have a cell column, the merging will be fine.

Congrats on the package being accepted to BioC!

Thanks,
Estella

[drighelli]

Hi @estellad,
thanks for the review and the update.

Works for me.

If you prefer, I'm going to test the new code into SpaceTrooper before merging it.

Thanks for the congrats, we are really happy the package has been accepted :)

Dario

[estellad]

Sounds good! Please let me know when you have finished the testing with a new commit, and then I will merge your PR?

Looking forward to see SpaceTrooper in OSTA 😃

Estella

[drighelli]

I'm doing some tests, and still is not working on my tiny data.

I'll keep you posted once I'll be able to fix everithing.

Otherwise we can keep the merfish and merscope separated.