Add chromatin mark data to example report

[bschilder]

@serachoi1230 could you add some chromatin mark data to the example vignette? (only has ATAC, DNAse data atm).

Here is the explanation of how I made/distributed the report. I had to use some tricks to around the size limit of vignettes.

1. Generate the example report and put it in the report folder here: https://github.com/neurogenomics/EpiCompare/tree/master/report

2. Usehtmltools::includeHTML to render the remotely-stored report within the vignette: https://github.com/neurogenomics/EpiCompare/blob/ee5dcb8906aea0a9f49a50550794e1b4b2afa5ec/vignettes/example_report.Rmd#L14

3. Let rworkflows generate the documentation site and render the vignette with the embedded example report: https://neurogenomics.github.io/EpiCompare/articles/example_report.html

[bschilder]

@serachoi1230 do you have an R script to generate the example report in report? (including data download/import steps) https://github.com/neurogenomics/EpiCompare/tree/master/report

We should include this code in the vignette, even if just as a comment that isn't run at the time of rendering vignettes.

[bschilder]

@serachoi1230 it looks like you accidentally deleted the reports folder on GitHub with your most recent push.

On GHA (and now locally and pulling your changes) this is causing the vignette example_report.Rmd to fail as it cannot find the file report/EpiCompare_example.html to render.

Given that this is rather complicated to manage in the long run, I think the best thing to do would be to upload the html file under the Releases part of the repo and render the file from there. That way, it won't have to sit in the main repo directory, and won't add too much to the overall package size: https://github.com/neurogenomics/EpiCompare/releases/tag/1.3.3

Can you please update the report with:

• The latest version of EpiCompare
• The chromatin data added.

[bschilder]

Related convo here:

148

Updated report has now been pushed to the gh-pages branch.