Question

affycoretools' plotPCA no longer can do 3D plot?

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Jenny Drnevich ★ 2.0k

@jenny-drnevich-2812

Last seen 8 days ago

United States

Hi Jim,

I've loved using many of your functions from affycoretools for gene expression data from any technology. However, after upgrading to R 3.2.0, it appears in the newest version of affycoretools (v. 1.40.0), the plotPCA function can no longer do a 3D plot? Did you have to remove this because plotPCA is now a BiocGenerics function? Is there perhaps an alternative function? I've always used the 2D and 3D plots in combination and found them to be a very useful tool, so I'm sad to lose the easy 3D functionality.

Thanks,

Jenny

affycoretools • 1.5k views

ADD COMMENT • link updated 9.7 years ago by James W. MacDonald 67k • written 9.7 years ago by Jenny Drnevich ★ 2.0k

score 1 · Answer 1 · 2015-04-21

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 4 days ago

United States

Hi Jenny,

I just did a fairly extensive refactoring of affycoretools, primarily to switch from using annaffy for HTML output to using ReportingTools. As part of that I tried to reduce the dependency tree, which is still pretty massive. But since I only used rgl for that one function, and I actually rarely do 3D PCA plots, I thought that would be a pretty reasonable dependency to remove.

I did not convert plotPCA() to a S4 function depending on the BiocGenerics function because a.) I am a bad man, and b.) I would be defining a generic for ExpressionSets and matrices, which I imagine many other packages are doing as well, so you will still have to do favoredpackage::plotPCA() to get the function you want, regardless of how I define it internally.

If you want, I can add that functionality back. The rgl package was just suggested anyway.

ADD COMMENT • link 9.7 years ago James W. MacDonald 67k

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Jim,

Tangential to the missing functionality, but of equal importance: I'm glad you've finally recognized and admitted to (a).

As we all know, admission of a problem is the first step required on the long road one must travel to fix it and now we can take this journey together. You've helped an enumerable number of people through your software contributions and sharing your knowledge in this forum[*], now let us help you.

[*] although, given your admission to (a), I'm sure you must have somehow hacked the system to give you 34k + points, but let's let bygones be bygones.

ADD REPLY • link 9.7 years ago Steve Lianoglou ★ 13k

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Ugh. I should have known that number was too large to be credible. I read 'Predictably Irrational' too late to realize that given the ability to cheat without the chance of being caught, most people still won't go 'whole hog'. But I do try to live by the motto that 'Nothing exceeds like excess', so I consider those types slackers.

ADD REPLY • link 9.7 years ago James W. MacDonald 67k

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Hi Jim, Yes, please add the 3D functionality back! I can imagine that the rgl 3D graphs wouldn’t work well with a shift to ReportingTools/shiny/knittr/R markdown –style reports, but I’ve resisted moving to those so far (mostly just no time to learn!). Thanks, Jenny From: James W. MacDonald [bioc] [mailto:noreply@bioconductor.org] Sent: Tuesday, April 21, 2015 10:56 AM To: Zadeh, Jenny Drnevich Subject: [bioc] A: affycoretools' plotPCA no longer can do 3D plot? Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""> User James W. MacDonald<https: support.bioconductor.org="" u="" 5106=""/> wrote Answer: affycoretools' plotPCA no longer can do 3D plot?<https: support.bioconductor.org="" p="" 66859="" #66865="">: Hi Jenny, I just did a fairly extensive refactoring of affycoretools, primarily to switch from using annaffy for HTML output to using ReportingTools. As part of that I tried to reduce the dependency tree, which is still pretty massive. But since I only used rgl for that one function, and I actually rarely do 3D PCA plots, I thought that would be a pretty reasonable dependency to remove. I did not convert plotPCA() to a S4 function depending on the BiocGenerics function because a.) I am a bad man, and b.) I would be defining a generic for ExpressionSets and matrices, which I imagine many other packages are doing as well, so you will still have to do favoredpackage::plotPCA() to get the function you want, regardless of how I define it internally. If you want, I can add that functionality back. The rgl package was just suggested anyway. ________________________________ You may reply via email or visit A: affycoretools' plotPCA no longer can do 3D plot?

ADD REPLY • link 9.7 years ago Jenny Drnevich ★ 2.0k

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OK. Version 1.40.1, should propagate within the next day or so. Or you can get from svn if you like.

ADD REPLY • link 9.7 years ago James W. MacDonald 67k