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Cna and putative driver coloring in expression tab #1377

Merged
merged 17 commits into from
Aug 23, 2018
Merged

Cna and putative driver coloring in expression tab #1377

merged 17 commits into from
Aug 23, 2018

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adamabeshouse
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@adamabeshouse adamabeshouse requested a review from alisman August 13, 2018 20:56
@adamabeshouse adamabeshouse force-pushed the expr-cna branch 4 times, most recently from 233517d to f13bd8b Compare August 13, 2018 22:31
alisman
alisman reviewed Aug 14, 2018
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src/pages/resultsView/ResultsViewPage.tsx
if (store.rnaSeqMolecularData.isComplete && store.studyIdToStudy.isComplete
&& store.mutations.isComplete && store.genes.isComplete && store.coverageInformation.isComplete) {
if (store.studyIdToStudy.isComplete
&& store.putativeDriverAnnotatedMutations.isComplete && store.genes.isComplete && store.coverageInformation.isComplete) {
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putative driver contains rnaseq and mutations data?

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what?

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oh, no I just rewrote it to use numericGeneMolecularDataCache as a data source

@jjgao jjgao temporarily deployed to cbioportal-frontend-pr-1377 August 15, 2018 21:34 Inactive
@jjgao jjgao had a problem deploying to cbioportal-frontend-pr-1377 August 16, 2018 17:23 Failure
@jjgao jjgao temporarily deployed to cbioportal-frontend-pr-1377 August 16, 2018 23:37 Inactive
@jjgao jjgao temporarily deployed to cbioportal-frontend-pr-1377 August 17, 2018 22:55 Inactive
@jjgao jjgao temporarily deployed to cbioportal-frontend-pr-1377 August 20, 2018 19:26 Inactive
@jjgao jjgao temporarily deployed to cbioportal-frontend-pr-1377 August 20, 2018 19:28 Inactive
@jjgao jjgao temporarily deployed to cbioportal-frontend-pr-1377 August 20, 2018 21:05 Inactive
@jjgao jjgao temporarily deployed to cbioportal-frontend-pr-1377 August 20, 2018 22:08 Inactive
@jjgao jjgao temporarily deployed to cbioportal-frontend-pr-1377 August 20, 2018 22:15 Inactive
@jjgao jjgao temporarily deployed to cbioportal-frontend-pr-1377 August 21, 2018 00:15 Inactive
@adamabeshouse
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adamabeshouse commented Aug 21, 2018 •
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  • reverse tick label angle
  • cbioTooltip class needs to be applied on Popover
  • reduce right padding when no legend, but still leave room for angled tick labels
  • move '* Driver annotations ... ' message outside borderedChart

Abeshouse, Adam A./Sloan Kettering Institute added 6 commits August 22, 2018 16:45
expression tab - cna and putative driver coloring
2332cfb 
Also in plots tab, determine render ordering using copy number change as well as mutation

Signed-off-by: Abeshouse, Adam A./Sloan Kettering Institute <abeshoua@mskcc.org>
Do not show Sort By in expression tab w only one visible study
0e41020 
Signed-off-by: Abeshouse, Adam A./Sloan Kettering Institute <abeshoua@mskcc.org>
Update screenshots
5c91d30 
Signed-off-by: Abeshouse, Adam A./Sloan Kettering Institute <abeshoua@mskcc.org>
box plot - flatten labels for horizontal legend, put on bottom in exp…
c77c6e3 
…ression

Signed-off-by: Abeshouse, Adam A./Sloan Kettering Institute <abeshoua@mskcc.org>
box plot - dont wrap tick labels
d66cfb3 
Signed-off-by: Abeshouse, Adam A./Sloan Kettering Institute <abeshoua@mskcc.org>
Box plot - dont use zero values in calculating boxes
fc8caac 
Signed-off-by: Abeshouse, Adam A./Sloan Kettering Institute <abeshoua@mskcc.org>
Abeshouse, Adam A./Sloan Kettering Institute added 7 commits August 22, 2018 16:45
refine padding spec in boxplot and use in expression tab. shrink expr…
3bbb39f 
…ession box width to fit all tcga pancan

Signed-off-by: Abeshouse, Adam A./Sloan Kettering Institute <abeshoua@mskcc.org>
Adjust expression tooltips
f1ff8b9 
Signed-off-by: Abeshouse, Adam A./Sloan Kettering Institute <abeshoua@mskcc.org>
Adjustments to box plot padding
b68f81d 
Signed-off-by: Abeshouse, Adam A./Sloan Kettering Institute <abeshoua@mskcc.org>
box and scatterplot - multiple VictoryScatter elements to improve per…
d0f1f9c 
…formance

Split up data into multiple VictoryScatter elements, each with fixed style attributes
rather than style specified by functions of the data, which improves performance.

Signed-off-by: Abeshouse, Adam A./Sloan Kettering Institute <abeshoua@mskcc.org>
Handle render order in a different way
ada37f1 
Signed-off-by: Abeshouse, Adam A./Sloan Kettering Institute <abeshoua@mskcc.org>
plots tab - add cbioTooltip class to tooltips
eccf26c 
Signed-off-by: Abeshouse, Adam A./Sloan Kettering Institute <abeshoua@mskcc.org>
Expression tab - Move driver annotation message outside chart border
eccea81 
Signed-off-by: Abeshouse, Adam A./Sloan Kettering Institute <abeshoua@mskcc.org>
@jjgao jjgao had a problem deploying to cbioportal-frontend-pr-1377 August 22, 2018 21:19 Failure
@jjgao jjgao temporarily deployed to cbioportal-frontend-pr-1377 August 22, 2018 22:21 Inactive
@jjgao jjgao temporarily deployed to cbioportal-frontend-pr-1377 August 22, 2018 22:23 Inactive
Abeshouse, Adam A./Sloan Kettering Institute added 4 commits August 22, 2018 21:10
box and scatter plot - Reduce right padding when no legend is there
b8d6926 
Signed-off-by: Abeshouse, Adam A./Sloan Kettering Institute <abeshoua@mskcc.org>
box plot - Change tick label orientation
4b2b06c 
So that start of tick label is at tick point

Signed-off-by: Abeshouse, Adam A./Sloan Kettering Institute <abeshoua@mskcc.org>
box and scatter plot - Put cbioTooltip class on Popover
9e8b04e 
Signed-off-by: Abeshouse, Adam A./Sloan Kettering Institute <abeshoua@mskcc.org>
Update screenshots
64df615 
Signed-off-by: Abeshouse, Adam A./Sloan Kettering Institute <abeshoua@mskcc.org>
@alisman alisman merged commit e8a4723 into cBioPortal:master Aug 23, 2018
@adamabeshouse adamabeshouse deleted the expr-cna branch August 23, 2018 17:38
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@adamabeshouse @alisman @jjgao