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Update function logScalePossible for generic assay negative data #5084

Merged
merged 3 commits into from
Jan 15, 2025
Merged

Update function logScalePossible for generic assay negative data #5084

merged 3 commits into from
Jan 15, 2025

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TJMKuijpers
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This PR fixes the bug describe in this issue.

Now, when we select generic assay data with negative values, the logScalePossible does return false whereas before it would always return true.

Before:
image
Now:
image

@TJMKuijpers TJMKuijpers self-assigned this Jan 14, 2025
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@TJMKuijpers TJMKuijpers linked an issue Jan 14, 2025 that may be closed by this pull request
Plots tab bug: chart fails to render when generic assay data has negative values cBioPortal/cbioportal#11334
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@TJMKuijpers TJMKuijpers marked this pull request as ready for review January 15, 2025 08:25
@TJMKuijpers TJMKuijpers changed the title Update logScalePossible for generic assay negative data Update function logScalePossible for generic assay negative data Jan 15, 2025
@TJMKuijpers TJMKuijpers requested a review from inodb January 15, 2025 15:31
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@inodb if you want to recreate the issue on the public portal, this would be the steps:
Go to study gbm_cptac_2021 -> query ERBB2 -> go to plot, switch y axis to “mRNA expression FPKM UQ”, note that the “log scale” is not checked -> switch to “Z score of mRNA expression” -> switch back to “mRNA expression FPKM UQ”, note that the “log scale” is now checked -> switch to “Protein level - Phospoprotein abundance ratio”, now the chart fails.

I think the interesting part here is that this only occurs when you have select mRNA first.

@alisman alisman merged commit 6908c32 into cBioPortal:master Jan 15, 2025
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olzhasmukayev pushed a commit to olzhasmukayev/cbioportal-frontend that referenced this pull request Jan 16, 2025
@TJMKuijpers @olzhasmukayev
Update function logScalePossible for generic assay negative data (cBi…
d705fa6 
…oPortal#5084)

* Update logScalePossible for generic assay negative data

* make sure that return type is always boolean

* Add test for negative and positive data of type number
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@inodb inodb Awaiting requested review from inodb

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Plots tab bug: chart fails to render when generic assay data has negative values
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@TJMKuijpers @alisman