Publish WGCNA example! #384
Conversation
* Put in basic changes: navbar, dict, snakefile, Rmd * More polishing and info and refs * Update file paths * Bring back docker changes * Add to dictionary * Add a couple refs * Add ref and other little things * Revert "Add ref and other little things" This reverts commit 7560c2a. * Address straightforward comments from cbethell * Add ref * Add more refs and re-render * Remove that extra part that should only be in part2 not here * Incorporate jashapiro review * Shorten up some more comments * rowSums!! * Get rid of tibble step and change wording
* Put in basic changes: navbar, dict, snakefile, Rmd * More polishing and info and refs * Update file paths * Bring back docker changes * Add to dictionary * Add a couple refs * Add next steps * Add some polishing and refs * Address the straightforward items from cbethell 's review * Incorporate jashapiro review from #358 * Style Rmds * Bring over part1 changes and re-render * Edit things based on jashapiro review Co-authored-by: GitHub Actions <[email protected]>
* Put in basic changes: navbar, dict, snakefile, Rmd * More polishing and info and refs * Update file paths * Bring back docker changes * Add to dictionary * Add a couple refs * Add next steps * Add some polishing and refs * Address the straightforward items from cbethell 's review * Incorporate jashapiro review from #358 * Style Rmds * Bring over part1 changes and re-render * Add last set of steps * Push this partcular plot version in case we wanna come back to it * Commit this multiple module pheatmap in case I want to return to it * ComplexHeatmap is mostly wrangled * It's working! * Save to PDFs * Fix color function and re-render * Add outlier thing * Revert "Add outlier thing" This reverts commit 8b9d57c. * Add ref for ComplexHeatmap * Incorporate jashapiro review and rerender * Remove standardize_genes option * Wrap up those last few typo things Co-authored-by: GitHub Actions <[email protected]>
* Put in basic changes: navbar, dict, snakefile, Rmd * More polishing and info and refs * Update file paths * Bring back docker changes * Add to dictionary * Add a couple refs * Add next steps * Add some polishing and refs * Address the straightforward items from cbethell 's review * Incorporate jashapiro review from #358 * Style Rmds * Bring over part1 changes and re-render * Add last set of steps * Push this partcular plot version in case we wanna come back to it * Commit this multiple module pheatmap in case I want to return to it * ComplexHeatmap is mostly wrangled * It's working! * Save to PDFs * Fix color function and re-render * Add outlier thing * Style Rmds * Re-rendered html * switch the whole outlier thing to just a comment * re-render after staging merge Co-authored-by: GitHub Actions <[email protected]>
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Some spelling errors are back? https://github.com/AlexsLemonade/refinebio-examples/pull/384/checks?check_run_id=1480673832 |
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I was assuming you would do the other changes first? My guess is that there are dictionary changes in other PRs. |
It seemed easiest to cherry pick example's commits since those are all properly squashed. And then when we get to #383 It should only have the "other changes" left. (So I can do this same thing for GSEA and GSVA examples). |
In general yes, but since a lot of those changes expect earlier ones, I would for now do those first. My thought was to get all the messy commits done first, then move on to the nice modular and squashed ones. I was thinking you would start with a new branch to do what was in #383, but without WCGNA. Then we do WCGNA to test the future process with squashed commits. |
AH. Yeah, I suppose that makes sense. Let me try this out then. |
* Move order of install for WGCNA * warn moar
Changes Being Published
This is a test to only add WGCNA by itself
I made a branch off of master and cherry picked these WGCNA commits.
List of Commits/PR's Included
Link to html Preview
For reviewing purposes, you can take a browse through htmlpreview: http://htmlpreview.github.io/?https://github.com/AlexsLemonade/refinebio-examples/gh-pages-stages/01-getting-started/getting-started.html
Publishing Checklist:
Does everything look good using html preview -- having taken a particularly close look at any new html files?
Have any new examples been added to the refinebio-examples feedback survey? Ideally, don't click publish until this PR is merged (changes are autosaved).