How to best share output with collaborators?

[guidohooiveld]

Hi, I just saw your publication in BMC Bioinformatics on GeneTonic, and I would like to say thanks for developing such nice project!

I am playing now with the sample files and code you provided, and everything is working nicely.

In the end I obviously would like to use it with my own data sets. I also analyze datasets for coworkers (that are not very familiar with R/Bioconductor etc). Therefore I was wondering what the best way is to share the interactive GeneTonic output with them. Ideally I would like to send them e.g. the HTML file (+ associated content) so they can interactively explore the results themselves on their own computer. So as a test I naively saved the 'Shiny session' in Firefox as HTML, and then opened it in Chrome, to find out that this is not working... So, do you have any suggestions on how to do this?

Please note that I don't know anything about Shiny apps.... so it might very well be that (hopefully!) I missed something obvious, or that what I want is rather not possible...

Thanks! G

[federicomarini]

Hi there Guido, Thanks for the kind words, it is always a pleasure to open up an issue and see it is indeed not a bug report 😬

More than saving/sharing the shiny session, I would recommend you build up a GeneTonicList object, out of the components you might have passed singularly, and share that single object as an RDS file with your collaborators. While this still needs (at the moment) to be read in with a command before launching GeneTonic, this should contain pretty much everything you need to reproduce the things you have been doing live. Then, your collaborator would simply need to

library("GeneTonic")
my_gtl <- readRDS("path/to/that/file.RDS")
GeneTonic(gtl = my_gtl)

Then: if what you mean is to also keep track of the single elements you have been selecting live, and "showcase" them afterwards, that goes a little out of the scope of the simple loading of the RDS file. It is something that probably could be handled with shiny's bookmarking, but I was never too much into it to say I am confident it can really work...

Some options might be added (should be fairly simple, but I just jinxed it by writing it here 😉 ) for reloading the bookmarked features - tagging @AnnekathrinSilvia to keep track of this potential feature.

Hope this helps!

Federico