WGCNA Part 1: Set up #358

cansavvy · 2020-11-17T14:17:09Z

Analysis Purpose

This is part one of the WGCNA example covering the intro info and the basic set up.

Pull Request Stage

This is a Refined PR - needs review of details and polishing

It's draft PR was reviewed in #353

Strategy

This first PR is fairly straightforward as far as the steps. What is different from the draft PR is I tried to add more explanations and warnings about how to use this analysis -- things that I expect users will need to know if they change this to a different dataset.

Concerns/Questions for reviewers:

A lot of these first steps are pretty standard, so mainly the wording is the main thing to keep an eye on here.

Take a special look at the Purpose of this analysis and Using a different refine.bio dataset with this analysis? the rest of the intro information is standard info that I haven't changed much. It may be that as we continue with creating advanced topics examples we will find some of the other intro info (that's primarily from the template) may need to be changed. See this discussion #357.

Analysis Pull Request Check List (roughly in order):

Content checks

All {{BLANKS}} have been replaced with the correct content.
Sources are cited
Seed is set (if applicable) -- it will be next PR

Formatting Checks

Removed any manual numbering of sections.
Removed any instances of chunk naming.
Comments and documentation are up to date.
All links have been checked and are properly formatted.

Add datasets to S3

Added data and metadata files to S3.

Docker/Snakemake rendering components

Added the .html link to the navigation bar.
Any not yet added packages needed for this analysis have been added to the Dockerfile and it successfully builds.

This reverts commit 7560c2a.

cbethell

This looks good @cansavvy!!

Just have a few minor comments and a question around your minimum counts cutoff. Otherwise, this shaping up nicely 👍

04-advanced-topics/network-analysis_rnaseq_01_wgcna.Rmd

cansavvy · 2020-11-18T20:35:17Z

Keeping in mind that I haven't fully reworked the eigengene explanation (I'm going to see if Josh has ideas for how to explain this right as well as see if I am understanding eigengenes correctly), do you want to see if the rest of your comments are addressed well enough, @cbethell ?

I may bug you again about the eigengene thing to see if its clearer later. 😬

cansavvy · 2020-11-19T13:19:37Z

@jashapiro, as you've probably noticed by my mention of your name above, I was going to ask for your help on explaining eigengenes (as well as reviewing the rest). I thought/think I understood them to be akin to eigenvalues but now I'm wondering if they are more like the first principal component of PCA. I am unsure what the most brief but most intuitive way to explain (partially because I'm shaky on the concept myself). What's a good way to explain this without getting too in the weeds?

Here's the only place I can find eigengenes explained:
Alter et al, 2000.pdf

jashapiro · 2020-11-19T13:35:12Z

@jashapiro, as you've probably noticed by my mention of your name above, I was going to ask for your help on explaining eigengenes (as well as reviewing the rest). I thought/think I understood them to be akin to eigenvalues but now I'm wondering if they are more like the first principal component of PCA. I am unsure what the most brief but most intuitive way to explain (partially because I'm shaky on the concept myself). What's a good way to explain this without getting too in the weeds?

Here's the only place I can find eigengenes explained:
Alter et al, 2000.pdf

Yeah, I was going to work on that today (already assigned myself!). But while I am writing a little thing here: the 1st principal component axis is also the 1st eigenvector (after transformation, usually), so you are not totally wrong! (But eigengenes are a bit different... more later).

cbethell

The updates look great @cansavvy!

Just left a comment below re some additions I believe snuck their way in.

04-advanced-topics/network-analysis_rnaseq_01_wgcna.Rmd

jashapiro

This looks good! I like the level of introductory explanation that you added, and just had some small thoughts on clarification in that section

The other suggestion I have is some simplification in the setup calculations: do matrix calculations while we have a matrix, and before we convert it to a ddseq object that we have to pull data back out of..

It looks like I left a number of comments on a section that got deleted (and I was thinking should be in the next PR anyway!) Feel free to apply those to that PR!

04-advanced-topics/network-analysis_rnaseq_01_wgcna.Rmd

jashapiro · 2020-11-19T14:18:49Z

04-advanced-topics/network-analysis_rnaseq_01_wgcna.Rmd

+WGCNA uses a series of correlations to determine what genes are expressed together in your data set. 
+This is a fairly intuitive approach to gene network analysis which is pretty widely used for microarray (as well as RNA-seq). 
+
+As output, WGCNA gives groups of co-expressed genes as well as an eigengene x sample matrix (where eigengenes contain the summarized variance for a group of co-expressed genes) [@Alter2000; @Langfelder2007]. 


I actually think this is fine, with a small change.

I would drop the Alter reference; their eigengenes are actually a bit different, as they are based on reducing the full data set, not a subset of genes. Basically: the Alter version is to take the each principal component of the full matrix, and call it an eigengene. So if you use 100 PCs, you get 100 eigengenes. The Langfelder approach is to define modules through the coexpression network, then take the 1st (and only 1st) principal component of the expression matrix containing only the genes in a module as an eigengene. This works because we already know that the genes are highly correlated, so we can summarize them well with just that one measure.

One thing worth distinguishing is that an "eigengene" and the values of each sample are two different things... the former defines the axis of the primary variation, the latter the position of each sample along that axis.

Suggested change

As output, WGCNA gives groups of co-expressed genes as well as an eigengene x sample matrix (where eigengenes contain the summarized variance for a group of co-expressed genes) [@Alter2000; @Langfelder2007].

As output, WGCNA gives groups of co-expressed genes as well as an eigengene x sample matrix (where the values for each eigengene represent the summarized expression for a group of co-expressed genes) [@Langfelder2007].

their eigengenes are actually a bit different

I think this may be part of my problem interpreting things, I've seen the word eigengene used in several contexts but no clear definition stated overall.

Thanks for the clarification.

04-advanced-topics/network-analysis_rnaseq_01_wgcna.Rmd

jashapiro · 2020-11-19T14:47:02Z

04-advanced-topics/network-analysis_rnaseq_01_wgcna.Rmd

+Extract the normalized counts to a matrix and transpose it so we can pass it to WGCNA. 
+
+```{r}
+# First we are going to retrieve the normalized data from the `DESeqDataSet` object using the `assay()` function


Again, careful about long comment lines.

Womp womp. I think this will be a pattern for us when we work on #289

04-advanced-topics/network-analysis_rnaseq_01_wgcna.Rmd

cansavvy · 2020-11-19T17:47:09Z

I think your comments have been addressed, @jashapiro. (Only taking into account the truly part 1 items -- whoops on my part . I made changes on part2 where needed but we can address that later).

If you think the data frame manipulation changes are good, I'll file an issue that we should change that elsewhere where applicable. It is shorter so that's good.

04-advanced-topics/network-analysis_rnaseq_01_wgcna.Rmd

jashapiro

Looks good to me, just a couple little comments/suggestions.

04-advanced-topics/network-analysis_rnaseq_01_wgcna.Rmd

* 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 <actions@github.com>

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* 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 <actions@github.com>

* 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 <actions@github.com>

* 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 <actions@github.com>

* 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 <actions@github.com>

* Adding in some style with css * Use css magic * Try making the navbar blue * Add survey link * Make font smaller * Need a comma * Change to normalizePath * normalizepath separate step references.bib * Move references.bib to component folder * Update github actions to reflect staging branch (#311) * Update github actions to reflect staging branch * Add libglpk40 to Dockerfile * Make it gh-pages-stages! * Remove dockerfile change that should have been on its own all along * Does this work? * Declare a uses * Switch how env is declared * Force it to run so we can test it * try no curly brackets * What's up with the branch * Move to bash if instead * Need quotes? * forgot a `then` * Try dollar signs * Doesn't like the `.`? * Use curly brackets * Try ${GITHUB_REF} * Try ${BRANCH_NAME} * try ${GITHUB_REF#refs/*/} * use jashapiro suggestion * Change to base ref * Change back to `github.ref` * Get rid of PR `on:` * Try another test * Docker dep fix: Add lib package 40 thing that clusterprofiler needs (#316) * Add lib package 40 thing that clusterprofiler needs * Try adding options(warn = 2) * Test if options(warn =2) means it breaks like it should * Revert "Test if options(warn =2) means it breaks like it should" This reverts commit d9f688f68448ef69fe4c1caa48af23051cd7f4e3. * Revert "Try another test" This reverts commit 845cf1aff92ea7b83f402bbefd563562b44e5eac. * Add google analytics to renderings (#314) * Try adding google analytics * Add to header using includes * temporary file snuck in there * Restore master version so they aren't in the review * Let's call an html file and html file * Docker dep fix: Add lib package 40 thing that clusterprofiler needs (#316) * Add lib package 40 thing that clusterprofiler needs * Try adding options(warn = 2) * Test if options(warn =2) means it breaks like it should * Revert "Test if options(warn =2) means it breaks like it should" This reverts commit d9f688f68448ef69fe4c1caa48af23051cd7f4e3. * Only push if we are in master. For simplicity, we will now run this even if the dockerfile hasn't changed. * Add test target * test staging workflow with this branch * back to latest tag * Try separate push step * change tags to test push * Revert "change tags to test push" This reverts commit 6a38574d312cee82c90c3c036ac9033f9af7f7ec. * Remove this branch from triggers * Push staging, retag and push master Okay, so the branch name is now inaccurate, but that is fine... * Made ccs modifications, added logo file Made changes to css/navbar.html Tried to add the logo but it but it cuts out and not sure how to make it decent. * Resolve render-notebooks.R conflict * Remove testing html from file diff * uncommented mobile nav * Update scripts/render-notebooks.R * Add some issue templates (#319) * Add some rough draft issue templates * Incorporate cbethell review * Get rid of `Other` labels that aren't useful * Update diagrams showing how microarray/RNA-seq work (#326) * Mechanics for CSS file and navbar add feedback URL (#303) * Adding in some style with css * Use css magic * Try making the navbar blue * Add survey link * Make font smaller * Need a comma * Change to normalizePath * normalizepath separate step references.bib * Move references.bib to component folder * Made ccs modifications, added logo file Made changes to css/navbar.html Tried to add the logo but it but it cuts out and not sure how to make it decent. * Resolve render-notebooks.R conflict * Remove testing html from file diff * uncommented mobile nav Co-authored-by: dvenprasad <dv.prasad991@gmail.com> * Update microarray and RNAseq overview figures - add context re figures - change .jpg to .png for consistency * Revert "Mechanics for CSS file and navbar add feedback URL (#303)" This reverts commit 8b81fdd96eeecf1d0e479d7908376b8e57dc356d. * update links to diagrams * @dvenprasad updated figure spacing * add the right updated figure * replace section of link to figures with updated commit id * incorporate @cansavvy's suggested changes Co-authored-by: Candace Savonen <cansav09@gmail.com> Co-authored-by: dvenprasad <dv.prasad991@gmail.com> * Adding basic footer (#307) * It works! * Add feedback url * Mechanics for CSS file and navbar add feedback URL (#303) * Adding in some style with css * Use css magic * Try making the navbar blue * Add survey link * Make font smaller * Need a comma * Change to normalizePath * normalizepath separate step references.bib * Move references.bib to component folder * Made ccs modifications, added logo file Made changes to css/navbar.html Tried to add the logo but it but it cuts out and not sure how to make it decent. * Resolve render-notebooks.R conflict * Remove testing html from file diff * uncommented mobile nav Co-authored-by: dvenprasad <dv.prasad991@gmail.com> * Make the footer retrieve step consistent with others Co-authored-by: dvenprasad <dv.prasad991@gmail.com> * Updating CONTRIBUTING.md with instructions about staging -> master set up (#313) * Updating contributing with info about staging branch * Mechanics for CSS file and navbar add feedback URL (#303) * Adding in some style with css * Use css magic * Try making the navbar blue * Add survey link * Make font smaller * Need a comma * Change to normalizePath * normalizepath separate step references.bib * Move references.bib to component folder * Made ccs modifications, added logo file Made changes to css/navbar.html Tried to add the logo but it but it cuts out and not sure how to make it decent. * Resolve render-notebooks.R conflict * Remove testing html from file diff * uncommented mobile nav Co-authored-by: dvenprasad <dv.prasad991@gmail.com> * Add more details to CONTRIBUTING about cherry picks and etc * Add bit about html preview * Incorporate Josh comment and drop log.log * Add bit about a hotfixes to staging PRs * Incorporate jashapiro feedback * Incorporate a few more bits of jashapiro feedback * Update doctoc * Make pull requests section H2 * Incorporate jashapiro suggestion to be make more specific branch names * Meh, we don't need <> * Change to use "publish" instead of "live" * Re DocToc * Add a bit more direction about PR base branches * Adjust links * Missed one link Co-authored-by: dvenprasad <dv.prasad991@gmail.com> * New PR templates to help with new process (#334) * Add basic templates * make it live PR template * Add html preview * Add one more "other" template * Minor edit * Polish up some things. Add "PR stage" * Minor edits * Implement cbethell review * Try a "main PR" strategy with links to the real PR templates (#337) * Get rid of headers and try a "main PR" thing. * Rearrange order * Links don't work per se * Try href strategy? * Update .github/PULL_REQUEST_TEMPLATE.md Co-authored-by: Chante Bethell <43576623+cbethell@users.noreply.github.com> Co-authored-by: Chante Bethell <43576623+cbethell@users.noreply.github.com> * Add contributing diagrams (#333) * Updating contributing with info about staging branch * Mechanics for CSS file and navbar add feedback URL (#303) * Adding in some style with css * Use css magic * Try making the navbar blue * Add survey link * Make font smaller * Need a comma * Change to normalizePath * normalizepath separate step references.bib * Move references.bib to component folder * Made ccs modifications, added logo file Made changes to css/navbar.html Tried to add the logo but it but it cuts out and not sure how to make it decent. * Resolve render-notebooks.R conflict * Remove testing html from file diff * uncommented mobile nav Co-authored-by: dvenprasad <dv.prasad991@gmail.com> * Add more details to CONTRIBUTING about cherry picks and etc * Add bit about html preview * Incorporate Josh comment and drop log.log * Add bit about a hotfixes to staging PRs * Incorporate jashapiro feedback * Incorporate a few more bits of jashapiro feedback * Add the PR diagrams * Add diagrams and some words about them to CONTRIBUTING.md * Couple minor edits * Update doctoc * Make pull requests section H2 * Incorporate jashapiro suggestion to be make more specific branch names * Meh, we don't need <> * Change to use "publish" instead of "live" * Update diagrams to say "publish" * re doctoc * Some polishing of wording * Make robot emoji a png so it renders * Update commit ids * A little more words * Make headlnes more parallel * Couple little updates * A couple more polishing items * Turn :warning: into :x: in diagrams * Update all img commit ids * Address comments from @cbethell 's review * One little wording update Co-authored-by: dvenprasad <dv.prasad991@gmail.com> * Make the "Other" PR template the default (#341) * Make the "Other" PR template the default * Use jashapiro's wording suggestions * Add timeline reminder to issue template (#342) * Pr 1 of 2: Add Microarray Pathway Analysis - GSEA example (#345) * Mechanics for CSS file and navbar add feedback URL (#303) * Adding in some style with css * Use css magic * Try making the navbar blue * Add survey link * Make font smaller * Need a comma * Change to normalizePath * normalizepath separate step references.bib * Move references.bib to component folder * Made ccs modifications, added logo file Made changes to css/navbar.html Tried to add the logo but it but it cuts out and not sure how to make it decent. * Resolve render-notebooks.R conflict * Remove testing html from file diff * uncommented mobile nav Co-authored-by: dvenprasad <dv.prasad991@gmail.com> * Making staging changes live (#329) * Adding in some style with css * Use css magic * Try making the navbar blue * Add survey link * Make font smaller * Need a comma * Change to normalizePath * normalizepath separate step references.bib * Move references.bib to component folder * Update github actions to reflect staging branch (#311) * Update github actions to reflect staging branch * Add libglpk40 to Dockerfile * Make it gh-pages-stages! * Remove dockerfile change that should have been on its own all along * Does this work? * Declare a uses * Switch how env is declared * Force it to run so we can test it * try no curly brackets * What's up with the branch * Move to bash if instead * Need quotes? * forgot a `then` * Try dollar signs * Doesn't like the `.`? * Use curly brackets * Try ${GITHUB_REF} * Try ${BRANCH_NAME} * try ${GITHUB_REF#refs/*/} * use jashapiro suggestion * Change to base ref * Change back to `github.ref` * Get rid of PR `on:` * Try another test * Docker dep fix: Add lib package 40 thing that clusterprofiler needs (#316) * Add lib package 40 thing that clusterprofiler needs * Try adding options(warn = 2) * Test if options(warn =2) means it breaks like it should * Revert "Test if options(warn =2) means it breaks like it should" This reverts commit d9f688f68448ef69fe4c1caa48af23051cd7f4e3. * Revert "Try another test" This reverts commit 845cf1aff92ea7b83f402bbefd563562b44e5eac. * Add google analytics to renderings (#314) * Try adding google analytics * Add to header using includes * temporary file snuck in there * Restore master version so they aren't in the review * Let's call an html file and html file * Docker dep fix: Add lib package 40 thing that clusterprofiler needs (#316) * Add lib package 40 thing that clusterprofiler needs * Try adding options(warn = 2) * Test if options(warn =2) means it breaks like it should * Revert "Test if options(warn =2) means it breaks like it should" This reverts commit d9f688f68448ef69fe4c1caa48af23051cd7f4e3. * Only push if we are in master. For simplicity, we will now run this even if the dockerfile hasn't changed. * Add test target * test staging workflow with this branch * back to latest tag * Try separate push step * change tags to test push * Revert "change tags to test push" This reverts commit 6a38574d312cee82c90c3c036ac9033f9af7f7ec. * Remove this branch from triggers * Push staging, retag and push master Okay, so the branch name is now inaccurate, but that is fine... * Made ccs modifications, added logo file Made changes to css/navbar.html Tried to add the logo but it but it cuts out and not sure how to make it decent. * Resolve render-notebooks.R conflict * Remove testing html from file diff * uncommented mobile nav * Update scripts/render-notebooks.R * Add some issue templates (#319) * Add some rough draft issue templates * Incorporate cbethell review * Get rid of `Other` labels that aren't useful * Update diagrams showing how microarray/RNA-seq work (#326) * Mechanics for CSS file and navbar add feedback URL (#303) * Adding in some style with css * Use css magic * Try making the navbar blue * Add survey link * Make font smaller * Need a comma * Change to normalizePath * normalizepath separate step references.bib * Move references.bib to component folder * Made ccs modifications, added logo file Made changes to css/navbar.html Tried to add the logo but it but it cuts out and not sure how to make it decent. * Resolve render-notebooks.R conflict * Remove testing html from file diff * uncommented mobile nav Co-authored-by: dvenprasad <dv.prasad991@gmail.com> * Update microarray and RNAseq overview figures - add context re figures - change .jpg to .png for consistency * Revert "Mechanics for CSS file and navbar add feedback URL (#303)" This reverts commit 8b81fdd96eeecf1d0e479d7908376b8e57dc356d. * update links to diagrams * @dvenprasad updated figure spacing * add the right updated figure * replace section of link to figures with updated commit id * incorporate @cansavvy's suggested changes Co-authored-by: Candace Savonen <cansav09@gmail.com> Co-authored-by: dvenprasad <dv.prasad991@gmail.com> Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org> Co-authored-by: dvenprasad <dv.prasad991@gmail.com> Co-authored-by: Chante Bethell <43576623+cbethell@users.noreply.github.com> * add first half of microarray GSEA example nb - add first part of new GSEA notebook example - update Snakefile - update navbar file - update `references.bib` - update `dictionary.txt` * revert commit that snuck in * revert second commit that snuck in * fix render notebooks merge conflict * incorporate cansavvy's review suggestions * add step handling duplicate ids - add note re using said approach * update comment * replace lfc with t-statistic value where mentioned * incorporate @cansavvy's review suggestions - fix typo - add sanity check when removing duplicates * replace `!duplicated()` with `dplyr::distinct()` * incorporate @jaclyn-taroni's review suggestions - add preview of `dr_hallmark_df` - add context where needed - adapt approach to removing duplicate gene ids * add a bit more context re removing dup gene IDs * use absolute value of t-statistic * Apply GSEA explanation suggestion from code review Co-authored-by: Jaclyn Taroni <jaclyn.n.taroni@gmail.com> * rerun snakefile to update rendered html Co-authored-by: Candace Savonen <cansav09@gmail.com> Co-authored-by: dvenprasad <dv.prasad991@gmail.com> Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org> Co-authored-by: Jaclyn Taroni <jaclyn.n.taroni@gmail.com> * Pr 2 of 2: Add Microarray Pathway Analysis - GSEA example (#347) * Mechanics for CSS file and navbar add feedback URL (#303) * Adding in some style with css * Use css magic * Try making the navbar blue * Add survey link * Make font smaller * Need a comma * Change to normalizePath * normalizepath separate step references.bib * Move references.bib to component folder * Made ccs modifications, added logo file Made changes to css/navbar.html Tried to add the logo but it but it cuts out and not sure how to make it decent. * Resolve render-notebooks.R conflict * Remove testing html from file diff * uncommented mobile nav Co-authored-by: dvenprasad <dv.prasad991@gmail.com> * Making staging changes live (#329) * Adding in some style with css * Use css magic * Try making the navbar blue * Add survey link * Make font smaller * Need a comma * Change to normalizePath * normalizepath separate step references.bib * Move references.bib to component folder * Update github actions to reflect staging branch (#311) * Update github actions to reflect staging branch * Add libglpk40 to Dockerfile * Make it gh-pages-stages! * Remove dockerfile change that should have been on its own all along * Does this work? * Declare a uses * Switch how env is declared * Force it to run so we can test it * try no curly brackets * What's up with the branch * Move to bash if instead * Need quotes? * forgot a `then` * Try dollar signs * Doesn't like the `.`? * Use curly brackets * Try ${GITHUB_REF} * Try ${BRANCH_NAME} * try ${GITHUB_REF#refs/*/} * use jashapiro suggestion * Change to base ref * Change back to `github.ref` * Get rid of PR `on:` * Try another test * Docker dep fix: Add lib package 40 thing that clusterprofiler needs (#316) * Add lib package 40 thing that clusterprofiler needs * Try adding options(warn = 2) * Test if options(warn =2) means it breaks like it should * Revert "Test if options(warn =2) means it breaks like it should" This reverts commit d9f688f68448ef69fe4c1caa48af23051cd7f4e3. * Revert "Try another test" This reverts commit 845cf1aff92ea7b83f402bbefd563562b44e5eac. * Add google analytics to renderings (#314) * Try adding google analytics * Add to header using includes * temporary file snuck in there * Restore master version so they aren't in the review * Let's call an html file and html file * Docker dep fix: Add lib package 40 thing that clusterprofiler needs (#316) * Add lib package 40 thing that clusterprofiler needs * Try adding options(warn = 2) * Test if options(warn =2) means it breaks like it should * Revert "Test if options(warn =2) means it breaks like it should" This reverts commit d9f688f68448ef69fe4c1caa48af23051cd7f4e3. * Only push if we are in master. For simplicity, we will now run this even if the dockerfile hasn't changed. * Add test target * test staging workflow with this branch * back to latest tag * Try separate push step * change tags to test push * Revert "change tags to test push" This reverts commit 6a38574d312cee82c90c3c036ac9033f9af7f7ec. * Remove this branch from triggers * Push staging, retag and push master Okay, so the branch name is now inaccurate, but that is fine... * Made ccs modifications, added logo file Made changes to css/navbar.html Tried to add the logo but it but it cuts out and not sure how to make it decent. * Resolve render-notebooks.R conflict * Remove testing html from file diff * uncommented mobile nav * Update scripts/render-notebooks.R * Add some issue templates (#319) * Add some rough draft issue templates * Incorporate cbethell review * Get rid of `Other` labels that aren't useful * Update diagrams showing how microarray/RNA-seq work (#326) * Mechanics for CSS file and navbar add feedback URL (#303) * Adding in some style with css * Use css magic * Try making the navbar blue * Add survey link * Make font smaller * Need a comma * Change to normalizePath * normalizepath separate step references.bib * Move references.bib to component folder * Made ccs modifications, added logo file Made changes to css/navbar.html Tried to add the logo but it but it cuts out and not sure how to make it decent. * Resolve render-notebooks.R conflict * Remove testing html from file diff * uncommented mobile nav Co-authored-by: dvenprasad <dv.prasad991@gmail.com> * Update microarray and RNAseq overview figures - add context re figures - change .jpg to .png for consistency * Revert "Mechanics for CSS file and navbar add feedback URL (#303)" This reverts commit 8b81fdd96eeecf1d0e479d7908376b8e57dc356d. * update links to diagrams * @dvenprasad updated figure spacing * add the right updated figure * replace section of link to figures with updated commit id * incorporate @cansavvy's suggested changes Co-authored-by: Candace Savonen <cansav09@gmail.com> Co-authored-by: dvenprasad <dv.prasad991@gmail.com> Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org> Co-authored-by: dvenprasad <dv.prasad991@gmail.com> Co-authored-by: Chante Bethell <43576623+cbethell@users.noreply.github.com> * add latter half of GSEA microarray example (includes GSEA steps) fix merge conflicts * add incode prompt * revert commit that snuck in * revert commit * set seed and re-run * incorporate some of the wording/context suggestions from review * rerun Snakefile * incorporate suggested changes re additional context/GSEA explanation * implement `top_n()` * add a bit more context for clarification re ES score * update GSEA explanation before gene ID conversion section * incorporate @cansavvy's wording suggestions * mimic "highly" -> "most" language * incorporate wording suggestions from code review * some re-structuring/re-wording based on review suggestions * update `dictionary.txt` file * incorporate @jaclyn-taroni's review suggestions Co-authored-by: Candace Savonen <cansav09@gmail.com> Co-authored-by: dvenprasad <dv.prasad991@gmail.com> Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org> * Delete intro Rmd and renumber (#355) * Try out intro and fix filenames * Undo intro paragraph for now. Too much * Missed one link to update in GSEA * Add words about Draft and Refined PRs to CONTRIBUTING.md (#361) * Explicitly discuss draft vs refine PRs in contrib * doctoc it * Remove asterisks * Refine wording * Use cbethell's wording suggestions * Make that one sentence more clear? * WGCNA Part 1: Set up (#358) * 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 7560c2a7cb861aaecefd8d241db209d8b3658989. * 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 * WGCNA Part 2: Running WGCNA (#360) * 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 <actions@github.com> * Add pathway analysis intro paragraph to microarray ORA (#356) * Try out intro and fix filenames * Undo intro paragraph for now. Too much * Add intro paragraph * Fix typo, add links * Incorporate cbethell review * Wording change from @envest * Fix WGCNA installation (#366) * Move order of install for WGCNA * warn moar * Pr 1 of 2: Add Microarray Pathway Analysis - GSVA example (#359) * Mechanics for CSS file and navbar add feedback URL (#303) * Adding in some style with css * Use css magic * Try making the navbar blue * Add survey link * Make font smaller * Need a comma * Change to normalizePath * normalizepath separate step references.bib * Move references.bib to component folder * Made ccs modifications, added logo file Made changes to css/navbar.html Tried to add the logo but it but it cuts out and not sure how to make it decent. * Resolve render-notebooks.R conflict * Remove testing html from file diff * uncommented mobile nav Co-authored-by: dvenprasad <dv.prasad991@gmail.com> * Making staging changes live (#329) * Adding in some style with css * Use css magic * Try making the navbar blue * Add survey link * Make font smaller * Need a comma * Change to normalizePath * normalizepath separate step references.bib * Move references.bib to component folder * Update github actions to reflect staging branch (#311) * Update github actions to reflect staging branch * Add libglpk40 to Dockerfile * Make it gh-pages-stages! * Remove dockerfile change that should have been on its own all along * Does this work? * Declare a uses * Switch how env is declared * Force it to run so we can test it * try no curly brackets * What's up with the branch * Move to bash if instead * Need quotes? * forgot a `then` * Try dollar signs * Doesn't like the `.`? * Use curly brackets * Try ${GITHUB_REF} * Try ${BRANCH_NAME} * try ${GITHUB_REF#refs/*/} * use jashapiro suggestion * Change to base ref * Change back to `github.ref` * Get rid of PR `on:` * Try another test * Docker dep fix: Add lib package 40 thing that clusterprofiler needs (#316) * Add lib package 40 thing that clusterprofiler needs * Try adding options(warn = 2) * Test if options(warn =2) means it breaks like it should * Revert "Test if options(warn =2) means it breaks like it should" This reverts commit d9f688f68448ef69fe4c1caa48af23051cd7f4e3. * Revert "Try another test" This reverts commit 845cf1aff92ea7b83f402bbefd563562b44e5eac. * Add google analytics to renderings (#314) * Try adding google analytics * Add to header using includes * temporary file snuck in there * Restore master version so they aren't in the review * Let's call an html file and html file * Docker dep fix: Add lib package 40 thing that clusterprofiler needs (#316) * Add lib package 40 thing that clusterprofiler needs * Try adding options(warn = 2) * Test if options(warn =2) means it breaks like it should * Revert "Test if options(warn =2) means it breaks like it should" This reverts commit d9f688f68448ef69fe4c1caa48af23051cd7f4e3. * Only push if we are in master. For simplicity, we will now run this even if the dockerfile hasn't changed. * Add test target * test staging workflow with this branch * back to latest tag * Try separate push step * change tags to test push * Revert "change tags to test push" This reverts commit 6a38574d312cee82c90c3c036ac9033f9af7f7ec. * Remove this branch from triggers * Push staging, retag and push master Okay, so the branch name is now inaccurate, but that is fine... * Made ccs modifications, added logo file Made changes to css/navbar.html Tried to add the logo but it but it cuts out and not sure how to make it decent. * Resolve render-notebooks.R conflict * Remove testing html from file diff * uncommented mobile nav * Update scripts/render-notebooks.R * Add some issue templates (#319) * Add some rough draft issue templates * Incorporate cbethell review * Get rid of `Other` labels that aren't useful * Update diagrams showing how microarray/RNA-seq work (#326) * Mechanics for CSS file and navbar add feedback URL (#303) * Adding in some style with css * Use css magic * Try making the navbar blue * Add survey link * Make font smaller * Need a comma * Change to normalizePath * normalizepath separate step references.bib * Move references.bib to component folder * Made ccs modifications, added logo file Made changes to css/navbar.html Tried to add the logo but it but it cuts out and not sure how to make it decent. * Resolve render-notebooks.R conflict * Remove testing html from file diff * uncommented mobile nav Co-authored-by: dvenprasad <dv.prasad991@gmail.com> * Update microarray and RNAseq overview figures - add context re figures - change .jpg to .png for consistency * Revert "Mechanics for CSS file and navbar add feedback URL (#303)" This reverts commit 8b81fdd96eeecf1d0e479d7908376b8e57dc356d. * update links to diagrams * @dvenprasad updated figure spacing * add the right updated figure * replace section of link to figures with updated commit id * incorporate @cansavvy's suggested changes Co-authored-by: Candace Savonen <cansav09@gmail.com> Co-authored-by: dvenprasad <dv.prasad991@gmail.com> Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org> Co-authored-by: dvenprasad <dv.prasad991@gmail.com> Co-authored-by: Chante Bethell <43576623+cbethell@users.noreply.github.com> * Add first half of microarray GSVA example notebook * add packages to Dockerfile and rerun * fix reference * add to navbar * remove mention of pheatmap * incorporate @jaclyn-taroni's suggestion on collapsing duplicates logic * incorporate cansavvy's review comments - fix logic combing rest of mapped data with the collapsed duplicates data - fix context around that logic * clarify/change some wording based on cansavvy's suggestions * incorporate single sample example of selecting max expression values * Push code that cbethell and I chatted through * Add to dictionary * Style Rmds * rerun Snakefile to update html file * Apply jaclyn-taroni's wording suggestions from code review Co-authored-by: Jaclyn Taroni <jaclyn.n.taroni@gmail.com> * incorporate the rest of jaclyn-taroni's review suggestions Co-authored-by: Candace Savonen <cansav09@gmail.com> Co-authored-by: dvenprasad <dv.prasad991@gmail.com> Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org> Co-authored-by: GitHub Actions <actions@github.com> Co-authored-by: Jaclyn Taroni <jaclyn.n.taroni@gmail.com> * WGCNA Part 3: DE and heatmaps (#363) * 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 8b9d57ce13ff2b6b6c5ddbb0169a794f6bbd36de. * 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 <actions@github.com> * WGCNA Part 4: Warn about Outliers (#364) * 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 <actions@github.com> * Microarray ORA Restructure Instruction (#377) * Some edits and adding other tutorials * Add more guidance about why pick ORA * A bit more word changing * A few more wording edits * Incorporating jashapiro review * Get rid of other GSEA mention * sessioninfo::session_info() * Put those two wording things in jashapiro mentioned * WGCNA Part 5: switch dataset (#379) * switch wording and dataset in general * Few more wording edits * Update dictionary; fix spelling errors * Re-render! * Change to 7 and incorporate jashapiro review * Also switch the most sig module! * Two comments from jashapiro review * Put the comments too * Style Rmds * Use all_of() to get rid warning * Style Rmds * Re-render Co-authored-by: GitHub Actions <actions@github.com> * Change pdf -> png and rereun (#382) * Pr 2 of 2: Add Microarray Pathway Analysis - GSVA example (#362) * Mechanics for CSS file and navbar add feedback URL (#303) * Adding in some style with css * Use css magic * Try making the navbar blue * Add survey link * Make font smaller * Need a comma * Change to normalizePath * normalizepath separate step references.bib * Move references.bib to component folder * Made ccs modifications, added logo file Made changes to css/navbar.html Tried to add the logo but it but it cuts out and not sure how to make it decent. * Resolve render-notebooks.R conflict * Remove testing html from file diff * uncommented mobile nav Co-authored-by: dvenprasad <dv.prasad991@gmail.com> * Making staging changes live (#329) * Adding in some style with css * Use css magic * Try making the navbar blue * Add survey link * Make font smaller * Need a comma * Change to normalizePath * normalizepath separate step references.bib * Move references.bib to component folder * Update github actions to reflect staging branch (#311) * Update github actions to reflect staging branch * Add libglpk40 to Dockerfile * Make it gh-pages-stages! * Remove dockerfile change that should have been on its own all along * Does this work? * Declare a uses * Switch how env is declared * Force it to run so we can test it * try no curly brackets * What's up with the branch * Move to bash if instead * Need quotes? * forgot a `then` * Try dollar signs * Doesn't like the `.`? * Use curly brackets * Try ${GITHUB_REF} * Try ${BRANCH_NAME} * try ${GITHUB_REF#refs/*/} * use jashapiro suggestion * Change to base ref * Change back to `github.ref` * Get rid of PR `on:` * Try another test * Docker dep fix: Add lib package 40 thing that clusterprofiler needs (#316) * Add lib package 40 thing that clusterprofiler needs * Try adding options(warn = 2) * Test if options(warn =2) means it breaks like it should * Revert "Test if options(warn =2) means it breaks like it should" This reverts commit d9f688f68448ef69fe4c1caa48af23051cd7f4e3. * Revert "Try another test" This reverts commit 845cf1aff92ea7b83f402bbefd563562b44e5eac. * Add google analytics to renderings (#314) * Try adding google analytics * Add to header using includes * temporary file snuck in there * Restore master version so they aren't in the review * Let's call an html file and html file * Docker dep fix: Add lib package 40 thing that clusterprofiler needs (#316) * Add lib package 40 thing that clusterprofiler needs * Try adding options(warn = 2) * Test if options(warn =2) means it breaks like it should * Revert "Test if options(warn =2) means it breaks like it should" This reverts commit d9f688f68448ef69fe4c1caa48af23051cd7f4e3. * Only push if we are in master. For simplicity, we will now run this even if the dockerfile hasn't changed. * Add test target * test staging workflow with this branch * back to latest tag * Try separate push step * change tags to test push * Revert "change tags to test push" This reverts commit 6a38574d312cee82c90c3c036ac9033f9af7f7ec. * Remove this branch from triggers * Push staging, retag and push master Okay, so the branch name is now inaccurate, but that is fine... * Made ccs modifications, added logo file Made changes to css/navbar.html Tried to add the logo but it but it cuts out and not sure how to make it decent. * Resolve render-notebooks.R conflict * Remove testing html from file diff * uncommented mobile nav * Update scripts/render-notebooks.R * Add some issue templates (#319) * Add some rough draft issue templates * Incorporate cbethell review * Get rid of `Other` labels that aren't useful * Update diagrams showing how microarray/RNA-seq work (#326) * Mechanics for CSS file and navbar add feedback URL (#303) * Adding in some style with css * Use css magic * Try making the navbar blue * Add survey link * Make font smaller * Need a comma * Change to normalizePath * normalizepath separate step references.bib * Move references.bib to component folder * Made ccs modifications, added logo file Made changes to css/navbar.html Tried to add the logo but it but it cuts out and not sure how to make it decent. * Resolve render-notebooks.R conflict * Remove testing html from file diff * uncommented mobile nav Co-authored-by: dvenprasad <dv.prasad991@gmail.com> * Update microarray and RNAseq overview figures - add context re figures - change .jpg to .png for consistency * Revert "Mechanics for CSS file and navbar add feedback URL (#303)" This reverts commit 8b81fdd96eeecf1d0e479d7908376b8e57dc356d. * update links to diagrams * @dvenprasad updated figure spacing * add the right updated figure * replace section of link to figures with updated commit id * incorporate @cansavvy's suggested changes Co-authored-by: Candace Savonen <cansav09@gmail.com> Co-authored-by: dvenprasad <dv.prasad991@gmail.com> Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org> Co-authored-by: dvenprasad <dv.prasad991@gmail.com> Co-authored-by: Chante Bethell <43576623+cbethell@users.noreply.github.com> * Add part two of GSVA microarray example notebook * update comment * update violin plot and its interpretation * add to `dictionary.txt` * apply significance and multiple hypothesis testing before plotting * Switching to northcott and a sina plot of one pathway * Style Rmds * Re-render it all * Adjust wording add tidbits about limma and re-render * Few more wording edits * Caught a few more little wording issues. Re-rendered * Remove Murat2008 ref * Restore the part 1 changes that got lost in the merge * incorporate most of jaclyn-taroni's suggested changes - create annotated results df using wide -> long method - update some wording/context re `mx.diff = TRUE` and what that means * remove outdated entries in `dictionary.txt` - remove unnecessary reference in `references.bib` * fix axis label * break up `annotated_results_df` steps * Apply suggestions from code review Co-authored-by: Jaclyn Taroni <jaclyn.n.taroni@gmail.com> * add reminder of `gsva_results` format - cite gsva package vignette - add more detail around "appropriate format" for plotting Co-authored-by: Candace Savonen <cansav09@gmail.com> Co-authored-by: dvenprasad <dv.prasad991@gmail.com> Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org> Co-authored-by: GitHub Actions <actions@github.com> Co-authored-by: Jaclyn Taroni <jaclyn.n.taroni@gmail.com> * Remove getting started zip file (#392) * ORA RNA-seq: Part 1 - The Set Up (#394) * Add the file. It works * Add components * re-render * Add review tags * Update wording around detectable genes * Add some words to dictionary.txt * re-render * Switch to PNG * Incorporating cbethell 's and envest 's review * Switch from using gene symbols to Entrez IDs * Isolate to just set up * Fix Typo * Polish the wording in a few places * Incorporate jashapiro reviews and remove tags * Port one wording change over to microarray ORA * One more wording edit * ORA RNA-seq: Part 2 - Run ORA and get results! (#395) * Add the file. It works * Add components * re-render * Add review tags * Update wording around detectable genes * Add some words to dictionary.txt * re-render * Switch to PNG * Incorporating cbethell 's and envest 's review * Switch from using gene symbols to Entrez IDs * Couple wording polishes * Copy over changes from #394 's review * Use jashapiro wording suggestions, delete tags * Add message = FALSE to mute chatty blocks (#398) * Add message=FALSE to library loading chunks * Rerender html files * Spell check fixes * rerender * add GSVA package to Dockerfile (#401) * Add rendering options via include.R (#402) * Add option to include R code in an early chunk * Add the include file when rendering * Change width to 70 * add example rerender * comment and naming changes * Update contributing.md with include file description * Add all rendered changes * GSVA for RNA-seq Part 1: Set up (#403) * Scrapbooking together an analysis * switch back to kcdf = "Gaussian" * Rearrange based on chat with Jackie * Fix the two things from jaclyn-taroni partial review * Few wording edits * Make the dup checks more relevant * Make PNG a bit bigger * incorporate most of jaclyn-taroni review comments * Try out the msigdbr list thing * Isolate to first parts of gsva * Editing explanations * Fix a couple spelling things * Incorporate jaclyn-taroni review and delete tags * Use `vst_df` * One more wording change * Remove that instance of "lists" that isn't really what we mean * Link citations in render (#407) * Add links to citations * Fix umlaut * Try different strategy for ortholog file download (#411) * Try different download strategy * Couple edits * Move link to before download * One other wording change * Editing/polish of microarray heatmap notebook (#409) * Intro edits * Heatmap edits * Render changes * Couple edits that didn't get saved * One more comment compaction. * Remove relative links * Add to microarray strengths * Carry over common comment changes (#414) * Carry over common comment changes * Style Rmds * White space change to force check Co-authored-by: GitHub Actions <actions@github.com> * Use same download.file strategy for ortholog RNA-seq example (#413) * Copy over changes from #411 but make it mouse * "automatically" gets deleted * GSVA for RNA-seq: Part 2 -- GSVA and a heatmap (#404) * Scrapbooking together an analysis * switch back to kcdf = "Gaussian" * Rearrange based on chat with Jackie * Fix the two things from jaclyn-taroni partial review * Few wording edits * Make the dup checks more relevant * Make PNG a bit bigger * incorporate most of jaclyn-taroni review comments * Try out the msigdbr list thing * Re-render * Update based on part 1 review * Add bit that shows overlaps * Make wording changes based on jaclyn-taroni review * Do some wording/explanation edits * RNA-seq DGE dataset switch (#416) * Introduce SRP123625 * Updating wording and some other items * Re-render it * Spell error fixes * jashapiro review suggestions * one more change and re-render * add part 1 of RNA-seq GSEA example notebook (take 2) (#419) * PCA polishing edits (#421) * Add principal component background Also shortened code lines and results tables * Add some more context and explanation of results * Updates to rnaseq PCA * Format and rerender * update screenshots * Apply suggestions from code review Co-authored-by: Candace Savonen <cansav09@gmail.com> * Don't call it a matrix it's been here for years * rerender Co-authored-by: Candace Savonen <cansav09@gmail.com> * Try out a different download strategy for ORA (#418) * Change download steps to download file * re-render * Spell error fixes * Use jashapiro wording * Use download.file for the three other notebooks (#422) * Bring over the GSEA changes * Add download.file() to the other three places * Found a typo * Fix two things cbethell mentioned in review * PR 2 of 2: Add RNA-seq Pathway Analysis - GSEA example (take 2) (#420) * add part 2 of RNA-seq GSEA example notebook (take 2) * rerun snakefile * incorporate jaclyn-taroni's review suggestions * rerun Snakefile to fix html output (#424) * Umap polish (#423) * UMAP polish edits * rendering * Apply suggestions from code review Co-authored-by: Candace Savonen <cansav09@gmail.com> * rerender * Move filtering to before DESeq2 object creation (#425) * re-render it * Further fix merge conflicts and re-render * Address jashapiro comments * Heatmap polish (#426) * Polishing edits to heatmap pages * Style and render * OSPL fix Co-authored-by: Candace Savonen <cansav09@gmail.com> * rownames -> row names * rerender all the things and delete a stray space * Polish differential exp microarray notebooks (#427) * Changes to differential exp microarray notebook * Spelling updates * Add comments and releveling, as suggested by @cansavvy * code formatting updates embrace the pipe * remove apeglm * Add some eBayes info! * polishing microarray multiple groups * Rerender everything * Split off multiple testing * Rerender * Minor Polish Diff Expr RNAseq (#429) * Minor polishing to RNAseq Diff Expr * render changes * Apply suggestions from code review Co-authored-by: Candace Savonen <cansav09@gmail.com> * render Co-authored-by: Candace Savonen <cansav09@gmail.com> * Polish the microarray ORA notebook (#430) * Update MSigDB section + rerender Also fixes long comments and rownames.print=FALSE * A few more edits to comments * Part 1: Add rownames.print = FALSE where its helpful (#431) * Add print.rownames = FALSE where its helpful * Apparently it doesn't affect design matrices * Push the htmls so that people can actually see them!!! * Polish the RNA-seq ORA example (#432) * Add the rownames.print = FALSE and re-render (#433) Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org> * Polish Microarray GSEA example (#434) * Polish wording and add introductory paragraphs * A bit more polishing * Apply suggestions from code review Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org> * Response to code review * Apply suggestions from code review Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org> * Propagate citation suggestion to multiple pathway notebooks * Missed these quotes * A few mapIds() items Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org> * Polish RNA-seq GSEA example (#437) * Polish wording and add introductory paragraphs * A bit more polishing * Apply suggestions from code review Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org> * Response to code review * Apply suggestions from code review Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org> * Propagate citation suggestion to multiple pathway notebooks * Missed these quotes * A few mapIds() items * Polish RNA-seq GSEA example * Missed a long comment * Update components/references.bib Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org> * Let the algorithm handle it Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org> * GHA: Slack us if Docker build or rendering fails (#438) * Add Slack notification to docker-build-push.yml * Add Slack notification to docker-build.yml * Add branch for testing * Add library load of package not installed * Revert "Add library load of package not installed" This reverts commit 4e83ed1e104f0760db40752f9bc9e641f916d374. * Revert "Add branch for testing" This reverts commit 06073504426dc1903cf46bb99cc65a3a91894a3c. * Polish Ensembl Gene ID conversions (bonus reference updates!) (#435) * Polish wording and add introductory paragraphs * A bit more polishing * Reference updates * ensembl gene id polish * Get out of here capital Refine.bio * No more bare dfs * Transfer changes to RNAseq (and some back) * Apply suggestions from code review Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org> * Response to code review * Some numeric updates * Add rendered files * render update * Citation update * Render updates * add comment & rerender Co-authored-by: Jaclyn Taroni <jaclyn.n.taroni@gmail.com> * Polish microarray GSVA example (#440) * Ignore the gene_sets directory * Polish the microarray GSVA example * Missed a couple mentions of GSEA * Borrow some polishing from #427 * Apply suggestions from code review Co-authored-by: Candace Savonen <cansav09@gmail.com> * Newline in intro paragraph everywhere * Add note about model organisms with GSVA Link to RNA-seq GSVA example * Rerender notebooks Co-authored-by: Candace Savonen <cansav09@gmail.com> * Polishing Ortholog notebooks (#436) * Polish wording and add introductory paragraphs * A bit more polishing * Reference updates * ensembl gene id polish * Get out of here capital Refine.bio * No more bare dfs * Transfer changes to RNAseq (and some back) * Apply suggestions from code review Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org> * Response to code review * Some numeric updates * Add rendered files * render update * Citation update * Add polishing for ortholog examples * Transfer intro sentence updates to related notebooks * more polish - remove duplicates from counts * Transfer changes to rnaseq * Rendering updates * other rendering updates * Render updates * Change ftp -> http for ftp.ebi As noted here: https://github.com/AlexsLemonade/refinebio-examples/issues/439#issuecomment-748721625 Confirmed that this does work as expected by rendering. * Add branch to docker-build-push.yml for render test * Apply suggestions from code review Co-authored-by: Candace Savonen <cansav09@gmail.com> * Clarify real genes * add some spelling words * Revert "Add branch to docker-build-push.yml for render test" This reverts commit 8e7b6ec868bab71c4ca0ec2f9b21e2be25df978b. * rendering * Caught an igor Co-authored-by: Jaclyn Taroni <jaclyn.n.taroni@gmail.com> Co-authored-by: Candace Savonen <cansav09@gmail.com> * Polish the RNA-seq GSVA example (#441) Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org> Co-authored-by: dvenprasad <dv.prasad991@gmail.com> Co-authored-by: Chante Bethell <43576623+cbethell@users.noreply.github.com> Co-authored-by: Jaclyn Taroni <jaclyn.n.taroni@gmail.com> Co-authored-by: GitHub Actions <actions@github.com>

cansavvy added 8 commits November 16, 2020 14:58

Put in basic changes: navbar, dict, snakefile, Rmd

8267148

More polishing and info and refs

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Merge branch 'cansavvy/wgcna-part1' into staging

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Merge branch 'staging' into cansavvy/wgcna-part1

2ee894a

Update file paths

aea879e

Bring back docker changes

0fbb1d3

Add to dictionary

d2f12f1

Add a couple refs

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cansavvy marked this pull request as ready for review November 17, 2020 14:41

cansavvy requested a review from cbethell November 17, 2020 14:47

Add ref and other little things

7560c2a

cansavvy mentioned this pull request Nov 18, 2020

WGCNA Part 2: Running WGCNA #360

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cansavvy changed the title ~~WGCNA PR1: Set up~~ WGCNA Part 1: Set up Nov 18, 2020

Revert "Add ref and other little things"

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cansavvy added 3 commits November 18, 2020 13:21

Address straightforward comments from cbethell

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Add more refs and re-render

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cansavvy requested a review from cbethell November 18, 2020 20:35

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Remove that extra part that should only be in part2 not here

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Incorporate jashapiro review

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cansavvy added a commit that referenced this pull request Nov 19, 2020

Incorporate jashapiro review from #358

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Shorten up some more comments

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rowSums!!

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Get rid of tibble step and change wording

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cansavvy merged commit 6e8579f into staging Nov 19, 2020

cansavvy deleted the cansavvy/wgcna-part1 branch November 19, 2020 19:03

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WGCNA Part 3: DE and heatmaps #363

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WGCNA Part 4: Warn about Outliers #364

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Publish 3 new examples (and some other changes) #383

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Publish WGCNA example! #384

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WGCNA Part 1: Set up #358

WGCNA Part 1: Set up #358

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	As output, WGCNA gives groups of co-expressed genes as well as an eigengene x sample matrix (where eigengenes contain the summarized variance for a group of co-expressed genes) [@Alter2000; @Langfelder2007].
	As output, WGCNA gives groups of co-expressed genes as well as an eigengene x sample matrix (where the values for each eigengene represent the summarized expression for a group of co-expressed genes) [@Langfelder2007].

WGCNA Part 1: Set up #358

WGCNA Part 1: Set up #358

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cansavvy commented Nov 17, 2020

Analysis Purpose

Pull Request Stage

Strategy

Concerns/Questions for reviewers:

Analysis Pull Request Check List (roughly in order):

Content checks

Formatting Checks

Add datasets to S3

Docker/Snakemake rendering components

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