Question: Posting a large interactive table online, supplementary to a publication?
1
gravatar for EduardoFox
5 months ago by
EduardoFox10
IBCCF / UFRJ
EduardoFox10 wrote:

I want to publish a transcriptome paper, along with interactive materials enabling readers to peruse the data behind the discussion. The R package 'plotly' enables rendering online-publishable tables that can be filtered & searched for specific entries.

I would like to publish such a table as supplementary to a paper (e.g. preprint version) however usually data repositories allow for uploading files and text.

Would anyone here know an official data repository with a format such that would enable publishing online an interactive table?

A good example of such a table is given in the link below:

https://butterlab.imb-mainz.de/flydev/?data=embryogenesis

Notes: I have tried recently with shiny-io but I ran into the issue that the server is only available to viewers for 24mins a month in the free account version. This is not enough to allow for few people perusing the large tables as supplementary materials.

Any ideas would be welcome.

Thanks in advance.

rna-seq shiny publishing R • 205 views
ADD COMMENTlink written 5 months ago by EduardoFox10

Can you talk your IT folks into running a shiny server for you? The free one is single-threaded, but doesn't have that time limitation.

ADD REPLYlink written 5 months ago by Devon Ryan88k

Perhaps I could, under ideal conditions. But as a postdoc in the 3rd world I think getting the department to set up a server for me will be quite hard. I will speak to my collaborators, nonetheless.

ADD REPLYlink written 5 months ago by EduardoFox10

Do you mean only a table, or as in your link - a shiyapp with plots, etc? And what bits of table is "interactive"? Is it not better to supply CSV, and users can use Excel or R, to apply further filters, pivots, etc.

ADD REPLYlink written 5 months ago by zx87546.8k

It is one very large table. The main interactive features are exactly filters and multi-paging to facilitate perusing the data. Like in the link, I think. Yes, I can provide the large table as well, but I believe very few readers do take the time to appreciate Supplementary data if it is not both attractive and readily accessible.

ADD REPLYlink written 5 months ago by EduardoFox10

A bit static solution would be to host the shiny code in GitHub, then anyone with R could run it through GitHub, e.g.:

runGitHub("myRepoName", "myUsername")
ADD REPLYlink written 5 months ago by zx87546.8k

I thought of Github Pages to host my tables, but apparently no shiny code works directly from there. In the example you provided, do you think it would be possible to have the app running directly from Gihub Pages?

ADD REPLYlink written 5 months ago by EduardoFox10
1

Relevant post at SO:

ADD REPLYlink modified 5 months ago • written 5 months ago by zx87546.8k

You can generate interactive non-Shiny HTML pages with htmlwidgets::saveWidget(). It's obviously more limited than a full Shiny app, but they can get fairly advanced. There are examples here: http://gallery.htmlwidgets.org/

ADD REPLYlink written 4 months ago by igor7.4k
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