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Add plotNMDS to miaViz #116

Merged
merged 16 commits into from
Jun 28, 2024
Merged

Add plotNMDS to miaViz #116

merged 16 commits into from
Jun 28, 2024

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thpralas
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This PR adds plotNMDS to miaViz (plotNMDS will be deprecated in the mia package).

This PR does not add documentation for plotNMDS because it is only a simple wrapper for scater::plotReducedDim and it would not fit under already existing man pages.

@thpralas thpralas mentioned this pull request Apr 17, 2024
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@thpralas
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This PR is related to microbiome/mia#517

@thpralas thpralas requested a review from TuomasBorman April 17, 2024 08:45
@TuomasBorman
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Can you add tests?

You can add same 3 lines that were removed in PR https://github.com/microbiome/mia/pull/517/files

@antagomir
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Seems good. Resolve conflicts.

thpralas and others added 2 commits May 22, 2024 10:51
@thpralas
merge devel
df85530 
Merge branch 'devel' of https://github.com/microbiome/miaViz into move_plotNMDS

# Conflicts:
#	NEWS
@TuomasBorman
Update plotNDMS.R
0e340c8
@antagomir
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up

@thpralas
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@TuomasBorman I think we agreed it is better for plotNMDS not to have its own manual page and that it does not fit in already existing manual pages in miaViz but I do not think it is possible to leave it without documentation. I tried to export it without documentation but I always get the following R CMD check warning:

Undocumented code objects:
    ‘plotNMDS’
  All user-level objects in a package should have documentation entries.
  See chapter ‘Writing R documentation files’ in the ‘Writing R
  Extensions’ manual.

@TuomasBorman
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Alright! You could add minimum documentation. Something like wrapper for plotReducedDim(). And just x parameter.

@TuomasBorman
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❯ checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'plotNMDS.Rd'
‘...’ ‘ncomponents’

@TuomasBorman TuomasBorman merged commit 867d9de into devel Jun 28, 2024
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@TuomasBorman TuomasBorman deleted the move_plotNMDS branch June 28, 2024 13:39
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@TuomasBorman TuomasBorman TuomasBorman approved these changes

@antagomir antagomir antagomir approved these changes

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@thpralas @TuomasBorman @antagomir