Polish RNA-seq GSEA example #437

jaclyn-taroni · 2020-12-18T14:40:37Z

Purpose

Polishing the RNA-seq GSEA example, building off of #434

Issue addressed

For the RNA-seq GSEA example, the following are being addressed:

Enforcing comment character length limit (Enforce code width limit #406)
Updating the section that said it was about clusterProfiler but was really about msigdbr (The "Getting familiar with clusterProfiler's options" section of ORA examples describes msigdbr #415)
Stopping row names from being printed for paged tables (Remove rownames from printed tables #428)
Adding the introductory paragraphs that are in every pathway analysis notebook (Add introductory paragraphs to microarray GSEA example, review text for RNA-seq GSEA example #354)

Also a fair bit of editing, but that's largely the same as what was in #434.

Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org>

…i/polish-rnaseq-gsea

…sh-rnaseq-gsea

jashapiro

Looks good (though I admit I didn't read too carefully, as it did seem that most of these changes were familiar from the last set.)

One bibliography fix, because I am oddly stringent on that.

components/references.bib

Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org>

* 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>

jaclyn-taroni and others added 14 commits December 16, 2020 14:42

Polish wording and add introductory paragraphs

af488fb

A bit more polishing

4eafeb2

Merge branch 'staging' into jaclyn-taroni/polish-microarray-gsea

d9daa4f

Apply suggestions from code review

294136f

Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org>

Response to code review

f5af911

Apply suggestions from code review

4d5868e

Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org>

Propagate citation suggestion to multiple pathway notebooks

b4bf736

Missed these quotes

fe64ea6

Merge branch 'jaclyn-taroni/polish-microarray-gsea' into jaclyn-taron…

93b331e

…i/polish-rnaseq-gsea

A few mapIds() items

0bb3f91

Merge branch 'jaclyn-taroni/polish-microarray-gsea' into jaclyn-taron…

6671144

…i/polish-rnaseq-gsea

Polish RNA-seq GSEA example

0728cfc

Merge remote-tracking branch 'origin/staging' into jaclyn-taroni/poli…

f678ca2

…sh-rnaseq-gsea

Missed a long comment

ccd412d

jaclyn-taroni requested review from cbethell and jashapiro and removed request for cbethell December 18, 2020 14:47

jashapiro approved these changes Dec 18, 2020

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jaclyn-taroni and others added 2 commits December 18, 2020 13:17

Update components/references.bib

f6e8177

Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org>

Let the algorithm handle it

4546438

jaclyn-taroni merged commit 6f6f02b into staging Dec 18, 2020

jaclyn-taroni deleted the jaclyn-taroni/polish-rnaseq-gsea branch December 18, 2020 21:42

jaclyn-taroni mentioned this pull request Dec 21, 2020

Add introductory paragraphs to microarray GSEA example, review text for RNA-seq GSEA example #354

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Polish RNA-seq GSEA example #437

Polish RNA-seq GSEA example #437

jaclyn-taroni commented Dec 18, 2020

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Polish RNA-seq GSEA example #437

Polish RNA-seq GSEA example #437

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jaclyn-taroni commented Dec 18, 2020

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