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lianos / sparrow

Take command of your set enrichment analyses.
https://lianos.github.io/sparrow/
MIT License
20 stars 1 forks source link

Reorder parameters in seas() to put `x` first. #5

Closed lianos closed 3 years ago

lianos commented 3 years ago

This function is really polymorphic over x, so this should come first.

The current function signature is:

seas <- function(gdb, x, design, contrast, ...)

but should really by

seas <- function(x, gdb, design = NULL, contrast = NULL, ...)

Let's bite this bullet before we release this into the wild.

carroj11 commented 3 years ago

Some fallout from this is that you also need to reorder any unnamed (by-position) arguments when calling seas(). This conversion is as above

https://github.com/lianos/multiGSEA/blob/85719e2b5388d425a3182c8611989a4b95fb75d1/R/multiGSEA.R#L162

https://github.com/lianos/sparrow/blob/9042f1609055e87cefad4033ac783603d947fc91/R/seas.R#L187

but now the calls to these are yet to be changed

https://github.com/lianos/multiGSEA.shiny/blob/ef24e4dda17ec6a79928e9cf7da7da57b5ee57eb/R/shiny-MultiGSEAResultContainer.R#L20

https://github.com/lianos/sparrow.shiny/blob/b536b6c307f49258adccd1275260313e074c67c5/R/shiny-SparrowResultContainer.R#L20

(image, since GH won't let me inline multiple sources)

multiGSEA_to_sparrow

This seems to cause some breakage. Credit to @maksymiuks for discovering this (we're trying to migrate).

jonocarroll commented 3 years ago

(back to my public account...) it appears the fix was all that was needed and we're successfully migrating. Thanks for the lightning fast patch ⚡ !