Hi everyone,
There was a lot of talk about shiny at BioC2013 and it seems like a
lot of people are using it for lots of different cool stuff.
Now we are at the point where some contributors want to add shiny apps
to Bioconductor as packages.
We had some discussion internally and decided that the
An answer to both of these issues is the use of R code. It should be
possible to drive shiny apps through the server, without the user's code
knowing the difference. And you've already thought of recording user
actions as R code. This would be an application of the command pattern, as
with undo/red
I agree with Dan on the need to be able to "save" analysis done in a Shiny
Bioconductor app, allowing someone later to reload the same state, and to
inspect a session and see what was done. Perhaps "save" and "load" buttons
should be present in the user interface of any Bioconductor Shiny app that
My perspective,
Clearly we are very interested in supporting reproducible research in
Bioconductor. Indeed, it is a core mission of the project. However, I
feel that Dan is placing a very high burden of proof on shiny apps in his
email, since it essentially says "because it is possible to potent
Hi Kasper,
On Mon, Jul 29, 2013 at 12:08 PM, Kasper Daniel Hansen
wrote:
> My perspective,
>
> Clearly we are very interested in supporting reproducible research in
> Bioconductor. Indeed, it is a core mission of the project. However, I
> feel that Dan is placing a very high burden of proof o
So here is something I came across in my code:
--t
On Jul 29, 2013, at 2:08 PM, Kasper Daniel Hansen
wrote:
> My perspective,
>
> Clearly we are very interested in supporting reproducible research in
> Bioconductor. Indeed, it is a core mission of the project. However, I
> feel that Dan i
Hi,
On Mon, Jul 29, 2013 at 1:38 PM, Tim Triche, Jr. wrote:
> So here is something I came across in my code:
>
>
>
> --t
... you came across a blank line or two? Fascinating ... :-)
-steve
--
Steve Lianoglou
Computational Biologist
Bioinformatics and Computational Biology
Genentech
_
Hi Winston,
On Mon, Jul 29, 2013 at 2:39 PM, Winston Chang wrote:
> Hi everyone -
>
> Great to hear from you all on your thoughts about Shiny. I've tried to
> answer some of Dan's questions below...
>
>
>>>
>>> 1) Testing shiny apps
>>>
>>> Typically, bioconductor packages have man page example
Yeah I'm good like that. What I was looking for is capture.output()
capture.output({ # {{{
clusts <- suppressWarnings(heatmap.3(t(tmp), scale="none", trace="none",
color.FUN=get(col.fun), dendrogram='none',
labCol=snps, kr
Hi,
I have been following this conversation with a lot of interest. I have
an R package with a shiny interface to another package recently
accepted in bioc-devel (rTRM). I was planning to submit it soon, as
the package is finished.
So my question is, should I hold the submission off until the
que
On Mon, Jul 29, 2013 at 4:46 PM, Dan Tenenbaum wrote:
> Hi Winston,
>
>
>
> On Mon, Jul 29, 2013 at 2:39 PM, Winston Chang wrote:
> > Hi everyone -
> >
> > Great to hear from you all on your thoughts about Shiny. I've tried to
> > answer some of Dan's questions below...
> >
> >
> >>>
> >>> 1) Te
I don't know how this actually works in practice. But conceptually, I think
of moving a slider in an Shiny app as possibly executing some R code. It
will be important for production quality code release that we are able to
test that this code works in a easy and portable way. I realize we may not
Right this is what I meant with the captureOutput() snippet. Perhaps the whole
reactive dispatch loop could be run to log instead of the clever force-
directed graph of closures updating that Joe showed off after presenting
Wednesday.
No good deed goes unpunished, and this suggests that loggin
[Resending as my message was bounced from bioc-devel the first time]
A large subset of Shiny apps can be thought of as purely functional
mappings from inputs to outputs, where the inputs are determined by the
user poking around the UI. I have always liked the idea of having a feature
in Shiny wher
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