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Add uniprot topology track #4004
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@jjgao @inodb @onursumer |
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Looks good, thank you! Just a few minor suggestions.
packages/react-mutation-mapper/src/component/track/UniprotTrack.tsx
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packages/react-mutation-mapper/src/component/track/UniprotTrack.tsx
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packages/react-mutation-mapper/src/component/track/UniprotTrack.tsx
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@leexgh looks great! Thank you. One minor point: the boxes are not middle aligned with the gray line. Could you fix that? |
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@@ -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?
cbioportal-frontend/packages/react-mutation-mapper/src/component/track/TrackItem.tsx
Line 11 in 3675a07
dim2?: number; // height if necessary |
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?
cbioportal-frontend/packages/react-mutation-mapper/src/component/track/Track.tsx
Line 220 in 6390038
dim2 = 22; |
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failing tests are not related, merging |
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, selectUniprot Topology
.SCN5A
is an example with complex domains, switch toEGFR
to see a less complex track.Screenshots
Expand
Tracks are expanded by default, click track name
Topology
to collapse or expand tracks.Collapse
Track Tooltip
Track description tooltip