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Add uniprot topology track #4004

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merged 3 commits into from
Nov 3, 2021
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leexgh
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@leexgh leexgh commented Oct 18, 2021

Fix: genome-nexus/genome-nexus#547

Goal

Add extracellular info from uniprot. For example their topology track shows cytoplasmic vs extracellular in the description of the tooltip. We group them by topological domains and adding as individual tracks.

Test

https://deploy-preview-4004--cbioportalfrontend.netlify.app/results/mutations?cancer_study_list=metastatic_solid_tumors_mich_2017&tab_index=tab_visualize&case_set_id=metastatic_solid_tumors_mich_2017_all&Action=Submit&gene_list=SCN5A%2520EGFR&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cfusion&geneset_list=%20

Click Add annotation tracks dropdown, select Uniprot Topology.
SCN5A is an example with complex domains, switch to EGFR to see a less complex track.

Screenshots

Expand

Tracks are expanded by default, click track name Topology to collapse or expand tracks.
image

Collapse

image

Track Tooltip

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Track description tooltip

image

@leexgh
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leexgh commented Oct 18, 2021

@jjgao @inodb @onursumer
Some questions about topology track:

  1. Do we want to add this track in cbioportal? (Initially we want to add this in genome nexus)
  2. How do you like the color? Tooltip? Track name?
  3. Suggestions for description?
    image

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Looks good, thank you! Just a few minor suggestions.

@leexgh leexgh force-pushed the uniprot-track branch 3 times, most recently from f600b55 to 6edeeea Compare October 27, 2021 06:26
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jjgao commented Oct 27, 2021

@leexgh looks great! Thank you. One minor point: the boxes are not middle aligned with the gray line. Could you fix that?

image

@@ -27,6 +27,7 @@ export type TrackItemSpec = {
label?: string;
color?: string;
tooltip?: JSX.Element;
rectHeight?: number; // set rectangle height (only works if itemType is RECTANGLE)
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Can we try using dim2 instead of introducing a new height prop?

Looks like it is hardcoded to 22 in Track.tsx. So maybe we can set its default value to 22, and set it to 15 for the new uniprot track?

@leexgh leexgh force-pushed the uniprot-track branch 3 times, most recently from 045a2ba to b1e76dd Compare November 2, 2021 17:07
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failing tests are not related, merging

@onursumer onursumer merged commit 60b5ab7 into cBioPortal:master Nov 3, 2021
@inodb inodb added the feature label Nov 9, 2021
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