Re: [Bioc-devel] plotPCA for BiocGenerics

I see the argument for separating plotting and computation. I don't see the argument for changing plotPCA to plot. base R has things that work either way; we all know hist(), boxplot() etc etc. And for this specific case there are (good) arguments for the fact that one could envision several plo

Re: [Bioc-devel] plotPCA for BiocGenerics

On Nov 1, 2014 1:29 PM, "Michael Love" wrote: > > As far as the proposal of using the plot() function for all plots, I > think for the biologists who are struggling already to get R going, > and to figure out what kinds of plots are possible, plotMA (and > knowing that the help is available at ?pl

Re: [Bioc-devel] More than 1 citation in landing page

- Original Message - > From: "Leonardo Collado Torres" > To: bioc-devel@r-project.org > Cc: "Jeff Leek" > Sent: Friday, October 31, 2014 4:05:11 AM > Subject: [Bioc-devel] More than 1 citation in landing page > > Hi, > > I'm wondering if it's possible to display more than 1 citation e

Re: [Bioc-devel] plotPCA for BiocGenerics

I guess I'm thinking now to move toward breaking up the PCA and plot in DESeq2, given that there is non-trivial computation going on, and then to leave plotPCA as a wrapper and to avoid breaking any user code. We had already moved this way a bit, in that in the current release, plotPCA has an argum

Re: [Bioc-devel] rhdf5 help

For the record: see https://support.bioconductor.org/p/62283 which includes a reply. > On 25 Oct 2014, at 21:07, Joseph Nathaniel Paulson > wrote: > > Hello, > > I'm in the process of writing a few wrappers for loading and writing out > files in the biom-format >