Add GWAS catalog to PheWeb #112

abought · 2018-09-25T07:24:10Z

Ticket: #17

Purpose

Add a GWAS catalog plot to PheWeb, based on an upcoming LZ.js release

TODO

Recommendations for discussion

Add test data that has a sample region with SNPs in the catalog (Peter)
Goncalo suggests making the GWAS catalog annotation track optional. (eg, rely solely on labels in the display options menu). Thoughts?

Known issues

Identify whether pointer-events:none is still needed, and if removal is a regression.
Since this updates LZ.js to the newest version, generally review app for breakages
Plot height is a bit too tall; let Peter sort that out.

Summary of changes

Replace in-repo LZ.js with a version from a CDN
DRY layouts to use extension mechanism
Region plots now use "association_catalog" instead of "standard_association" for their base plot layout (and appropriate child layouts, with modifications)
Change association source: remove override of a deprecated function, in favor of explicit namespaced field requests (revisit this)
Change LD source to eliminate redundant code- use subclassing for maintainability going forward

How to test this

Version 0.9.0 has not yet been released yet; we'll need to do that before PheWeb can be released! I've been testing with local static files, representing the tip of the LZ.js develop branch

abought · 2018-09-25T18:03:43Z

I've added back the field extraction mechanism. It does impose a namespacing restriction- this is still a change to PheWeb core behavior, but it makes it easier to use the same data source with all the other layers that already work that way.

Per the tooltip issue, I've traced this to pointer-events:none, the tooltip workaround. We're also seeing it with the exac link on genes tooltips in a modern pheweb. Will delegate that one to Peter as this was his workaround and he has more context.
http://pheweb.sph.umich.edu:5003/region/110.12/2:113925484-114325484

abought · 2018-09-26T03:03:34Z

Also fixed the phewas scatter plot tooltips. @pjvandehaar , when would be a good time to meet and parcel out the remaining tasks needed to move this forward?

abecasis · 2018-09-26T03:48:43Z

Great to see this happen. It would be great for PheWeb to serve as showcase of what locuszoom can do!

…

Sent from my iPhone

On Sep 25, 2018, at 3:24 AM, Andy Boughton ***@***.***> wrote: Ticket: #17 Purpose Add a GWAS catalog plot to PheWeb, based on an upcoming LZ.js release TODO Recommendations for discussion Add test data that has a sample region with SNPs in the catalog The catalog track only labels SNPs that are in high LD. Consider adding the "Make LD reference" link back to Pheweb assoc scatter plot tooltips, to encourage exploration. Known issues The PheWAS coloring mechanism has changed; update this so phewas plots are colored correctly GWAS catalog rug track tooltips are not properly clickable (can't click the GWAS catalog link; investigate pheweb overrides) Since this updates LZ.js to the newest version, generally review app for breakages The layout is slightly off kilter; revise and generally tweak positioning (some "spacer" panels were removed in the layout reconciliation, as their purpose was unclear) Summary of changes Replace in-repo LZ.js with a version from a CDN DRY layouts to use override mechanism Region plots now use "association_catalog" instead of "standard_association" for their base plot layout (and appropriate child layouts, with modifications) Change association source: remove override of a deprecated function, in favor of explicit namespaced field requests (revisit this) How to test this Version 0.9.0 has not yet been released yet; we'll need to do that before PheWeb can be released! I've been testing with local static files, representing the tip of the LZ.js develop branch (0a0df23) You can view, comment on, or merge this pull request online at: #112 Commit Summary Use CDN version for LZjs, and remove locally stored version. Updates for LZ.js 0.9 Reconcile duplicate region plot layout with LZjs core overrides File Changes M pheweb/conf_utils.py (1) M pheweb/serve/server.py (2) M pheweb/serve/static/region.js (610) M pheweb/serve/static/variant.js (29) D pheweb/serve/static/vendor/locuszoom-0.5.6-locuszoom.css (792) D pheweb/serve/static/vendor/locuszoom-0.5.6.app.js (8892) D pheweb/serve/static/vendor/locuszoom-0.5.6.vendor.min.js (6) M pheweb/serve/templates/gene.html (8) M pheweb/serve/templates/region.html (7) M pheweb/serve/templates/variant.html (9) Patch Links: https://github.com/statgen/pheweb/pull/112.patch https://github.com/statgen/pheweb/pull/112.diff — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

abought · 2018-10-04T21:03:34Z

No word from Peter as yet. In the interests of meeting ASHG deadlines, and recognizing that it's already been ~10 days, I'm going to put go ahead and make most of the layout and behavior changes originally marked "for discussion", plus a few other tweaks.

Some of the things I held off on could introduce possible regressions, but we can discuss the details after the fact. Will update more tomorrow.

abought · 2018-10-05T20:20:18Z

Tooltip functionality changed to support more granular hyperlinks (not just "click on dot to go to phewas").

Still need to identify test data with SNPs in the GWAS catalog; Peter would be more efficient at adding this. This concludes my current queue of work for PheWeb integration until we've looked over the direction and design plan.

sgagliano · 2018-10-05T20:52:37Z

Thanks Andy for all your work on this feature.
Peter, when are you able to address this PR?

Use a config variable to inject version into templates. Ideally we would use a true package management/asset build tool instead; this is admittedly a bit of a hack.

Represents bare minimum changes to restore core functionality.

This removes the "get all assoc fields" functionality, pending discussion/ updates to use the new data chain refactor. The hack bypassed source namespacing (which hampered reuse of existing layouts). Primary use case seems to be arbitrary tooltips; req't needs clarification. [ci skip]

with namespacing support Also clean up some window.debug globals (see breakpoint debugging as alternative)

[ci skip]

- Make tooltip links clickable (remove pointer-events hack) - Add "Make LD ref var" link back to tooltips - Add "go to phewas" link to tooltips (since clicking directly does not do the trick) - Remove keys found in base layouts - DRY LD source via super call - Remove custom padding style, as this was leading to display artifacts

(TODO: Improve synthetic data so we can test this) [ci skip]

[ci skip]

abought · 2018-10-15T19:32:40Z

I've pushed (most of) the changes from discussion branch 8cdb7...pull-112-head#diff-007e08bf75bfe53b85b14034803e369c . These are intended as a companion to statgen/locuszoom#150.

I'll merge the LZ.js PR tonight barring any further requests.

abought · 2018-10-15T19:52:22Z

A note: tests are passing locally (after incorporating the test_all fix- thanks!)

They are failing on travis even after restarting the build, but the error message is opaque. Peter, have you seen that failure log before?

pjvandehaar · 2018-10-15T22:35:13Z

I’ll try a different gencode url later.

abought · 2018-10-15T22:59:45Z

Gencode url? I might be missing context here- what sort of different data do you need?

(Would any of the pending LZ data source changes be of use?)

abought · 2019-01-14T05:24:23Z

LocusZoom 0.9 was officially released in late December, containing several of the items requested/used by PheWeb.

What is the status of this PR as a possible candidate for merge? Does it need updating?

Given the historical timeline, I'll hold off on making revisions until I hear back, but help is available on that basis.

pjvandehaar · 2019-04-16T16:11:25Z

This is now on master.

abought force-pushed the feature/gh17-gwas-catalog branch from ef85bd1 to 2d7e8b4 Compare October 5, 2018 20:17

abought changed the title ~~[WIP] Add GWAS catalog to PheWeb~~ Add GWAS catalog to PheWeb Oct 6, 2018

abought added 14 commits October 12, 2018 10:23

Use CDN version for LZjs, and remove locally stored version.

e10ca23

Use a config variable to inject version into templates. Ideally we would use a true package management/asset build tool instead; this is admittedly a bit of a hack.

Updates for LZ.js 0.9

443d7ee

Represents bare minimum changes to restore core functionality.

Reimplement the Peter Field Addition System (PFAS)

20b103a

with namespacing support Also clean up some window.debug globals (see breakpoint debugging as alternative)

Fix phewas plot coloring- adjust for changes made post 0.5.6

2eff10b

[ci skip]

Fix phewas scatter label

5f72ba4

[ci skip]

Switch to CDN versions for as many libraries as possible

20b1d3d

Remove hard-coded reliance on a meaningless parameter

5504352

Add conditional catalog link to assoc tooltips

73eb056

(TODO: Improve synthetic data so we can test this) [ci skip]

Reduce guesswork by adding version to about page

5ea9a58

[ci skip]

LD fix + ctd layout simplification

81d8cf5

[ci skip]

Simplify imports + styles before scripts

4d2824f

[ci skip]

Put rug track at top of plot

fe5a2c3

[ci skip]

abought force-pushed the feature/gh17-gwas-catalog branch from 2971259 to 6b6971b Compare October 15, 2018 19:11

Plot height and layout fixes

1184558

abought force-pushed the feature/gh17-gwas-catalog branch from 6b6971b to 1184558 Compare October 15, 2018 19:30

pjvandehaar closed this Apr 16, 2019

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Add GWAS catalog to PheWeb #112

Add GWAS catalog to PheWeb #112

abought commented Sep 25, 2018 •

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pjvandehaar commented Apr 16, 2019

Add GWAS catalog to PheWeb #112

Add GWAS catalog to PheWeb #112

Conversation

abought commented Sep 25, 2018 • edited Loading

Purpose

TODO

Recommendations for discussion

Known issues

Summary of changes

How to test this

abought commented Sep 25, 2018

abought commented Sep 26, 2018 • edited Loading

abecasis commented Sep 26, 2018 via email

abought commented Oct 4, 2018

abought commented Oct 5, 2018

sgagliano commented Oct 5, 2018

abought commented Oct 15, 2018 • edited Loading

abought commented Oct 15, 2018

pjvandehaar commented Oct 15, 2018

abought commented Oct 15, 2018

abought commented Jan 14, 2019

pjvandehaar commented Apr 16, 2019

abought commented Sep 25, 2018 •

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abought commented Sep 26, 2018 •

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abought commented Oct 15, 2018 •

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