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lgatto / pRoloc

A unifying bioinformatics framework for organelle proteomics
http://lgatto.github.io/pRoloc/
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Explanation of Markers Matrix #62

Closed lmsimp closed 4 years ago

lmsimp commented 8 years ago

Somewhere in the vignette we need a section to explain that the markers stored in the feature data can either be a matrix or a character vector. Default if it's a matrix of markers is Markers. See mrkVecToMat and friends.

lmsimp commented 8 years ago

@lgatto Did we decide that is is okay to call mrkVecToMat inside new vis apps if input is not a matrix?

lgatto commented 8 years ago

Yes, doing that transparently is fine, as long as the user's data is not modified.

lmsimp commented 8 years ago

One issue, all the feature data columns in the new hyperlopit data, have names that begin with capitals (see data(hyperLOPIT2015) and fvarLabels(hyperLOPIT2015) in pRolocdata). This is very annoying for differentiating between vectors and matrices in the fData. There is the situation where I have a column called Markers which is a matrix, but I wish to plot the column SVM using my app, now, if I call mrkMatToVec with vfcol = "SVM" then I get an error as there is already Markers, I can specify a name for mfcol e.g. mfcol = "xxx" and plot that, this is all invisible and not seen my user, what would you suggest I call mfcol for these cases?

Yes, doing that transparently is fine, as long as the user's data is not modified.

When I call mrkMatToVec as discussed above, the users data is not altered as we do not return object. To be extra safe I can create a new MSnSet i.e. a copy of object but with the new Markers matrix appended, and use that for the interactive plotting, if in the future you envisage returning the original object?

lgatto commented 8 years ago

What would you suggest I call mfcol for these cases?

mfcol <- paste0("Markers", format(Sys.time(), "%a%b%d%H%M%S%Y"))

To be extra safe I can create a new MSnSet i.e. a copy of object

That's not needed. Just wanted to make sure it's not returned. Not sure about the future; no plans to return at this stage.