Updating iSEEnrich & iSEEinit #10
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On it soon! |
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See my comments in the specific location - the functionality add-ons are perfectly fine, well done in thinking that out!
We might need to fortify a bit the behavior, see the point where we could add some checks.
The other main thought - how often do we expect to have a list as input? Just asking because a vector is easy to check in its content (it has to be uniform), so would be the column of the dataframe. But a list could be a wild wild west of things that can be placed in the individual elements - a character, a vector, a data.frame, they would simply fit, but our unlisting would be brutalized. Are there specific use cases that give us back lists? Otherwise we could think of having only vectors and df supported
| clusters <- "Primary.Type" | ||
| groups <- "Secondary.Type" | ||
| reddim_type <- "PCA" |
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just a pointer again to note down what we can also do: Trigger the errors by selecting wrong values for such parameters - see the comment above about adding some extra checks at the beginning of the function
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thanks fede for the review 🙏 ! i included changes according to your suggestions. I also added a new parameter to call the features column name if |
…nal but leads to a cleaner console output/a full catching round
…iSEEfier into updating_iSEEnrich&iSEEinit
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I added a few edits in the tests, mainly to catch all console output types - such as "a message while still throwing an error afterwards", or some specific messages where these are thrown. Otherwise, LGTM 😉 |
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Ok, quick correction - we still need two small pieces to be updated, namely
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Done! I think now it's ready to merge and push into bioconductor repository 😃 |
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It is! The GHA failures are somehow due to the orgDb packages, so my guess is that this is transient (I think) |
@federicomarini would you please test the changes i made on the
iSEEinitandiSEEnrichfunctions? I changed thefeaturesinput ofiSEEinitto be anything (vector,list or dataframe). and foriSEEnrichI added a couple of plots for visualization. Thanks!!