Use of upload to synapse within package

[JamesPino]

In the function bagOfGenesEnrichment::plotTopGenesHeatmap, there is an argument for uploading to synapse. Should that be in the package? Will users be uploading their results to synapse or is that just for us. If just for us, I suggest we refactor that snippet out and create a separate function that we can call (export_results_to_synapse or something).

[sgosline]

it is just for us, perhaps we can pass in an argument in the markdowns?

[JamesPino]

Maybe just write a function that is separate?

mpnstXenoModeling::plotTopGenesHeatmap(
    drug.res,
    dds,
    pmap,
   figname,
    patients = c(goodsamps$Sample, badsamps$Sample),
    adjpval = 0.01,
  )

upload_to_synapse(fig_name,  parentID = 'syn25323411')

or the pipe %>%. Not sure if plots return an object that can be piped or not? Then the plot functions will be only for plotting, where anyone that wants to use/extend won't have to figure out synapse. Unless one of the goals is to encourage users to create synapse projects for their papers as well? If so, i'd probably still separate but document the steps so people can follow. I like the idea of people using synapse for the repo outputs. If that were the case, I think having a "download_project_files" for the project would be helpful too, that basically creates a visualization of r.md -> create synID, or r.md uses synID. This is off topic though.

[sgosline]

Sure, maybe we can prune everything out and put it in the synapseUtils.R file - this file is basically a mini synapseR that i've been porting around from project to project...