Modularize code

[mlbendall]

Check out this article.
http://shiny.rstudio.com/articles/modules.html

In order to work together effectively, and to make PathoStats as flexible as possible, we are going to need to write code that can be easily plugged into the PathoStats core. In the above article, the Rstudio folks have written up one possible way to do it, and I think it makes sense. I'm also open to other ideas.

I've started to do this for the Relative Abundance module, and I put an idea of what this might look like in this branch: https://github.com/mani2012/PathoStat/blob/newRAplots/R/relativeAbundance.R

My proposal is that each "top level" (relative abundance, diversity, differential expression, etc.) will live in its own file (within R/ directory). The module will be loaded into the shiny server. If you want to make additional tabs within that module, I would suggest that you create these as sub modules of the top-level module. This way all the code as well as UI elements for a tab/module are in one place and should be easy to change in the future.

[ecastron]

It makes sense to me. It'd be easier as we move forward and add more features. Going to give it a try with the longitudinal tab

[anfederico]

Here is a great barebones example of how one would modularize the code base.

https://github.com/daattali/advanced-shiny/tree/master/split-code

I think this project would benefit from this solution as the codebase is quite large. Some of the UI views are already modularized so maybe the best focus would be on making the server.R file modular (It's 2400 lines of code).

For example, each tab in the web-application would have a specific ui/server file.
ui_upload.R
server_upload.R
And so on for each tab...

Just a suggestion though, I know a big change like this takes considerable effort, but I would be willing to help! I'm sure it will benefit the project in terms of longevity.

[mlbendall]

I already began to modularize the code, it just never made it into master. See the diversity module branch.

I'd suggest putting both the UI and server functions into the same file, and call the functions uploadModule and uploadModuleUI.

[anfederico]

Ah nice, looks good. What else needs to be done to merge? is the testing going smoothly?

Edit: I see, it's far behind the master.