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Improve non-profiled gene panel links in oncoprint tooltip #4701

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merged 3 commits into from
Aug 31, 2023

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BasLee
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@BasLee BasLee commented Aug 17, 2023

Currently the gene panels in an oncoprint tooltip are marked red (instead of blue) when the gene is not on the panel.

However, just marking the gene panel with the color red is confusing for some users: what does this color mean? And why is my gene not showing up in the panel, when I click on it?

To improve the meaning of non-profiled gene panels, this PR removes the red color and adds a message that the gene is not on the gene panel.

image
New styling of gene panel without the current gene, including message

image
New styling when multiple patients are selected

@alisman
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alisman commented Aug 18, 2023

@BasLee this looks good. would you mind just putting a before and after screenshot in this PR so the product folks can quickly evaluate it?

@alisman
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alisman commented Aug 21, 2023

@inodb, @tmazor can you approve this from product perspective. see the screenshot above

@BasLee
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BasLee commented Aug 23, 2023

Instead of a message between brackets we could also formulate it like:
Gene Panels: Profiled in TESTPANEL1. Not profiled in TESTPANEL2.
Any preference? @inodb @alisman

@BasLee BasLee changed the title Add strike-through and message to non-profiled gene panels in oncoprint tooltip Improve non-profiled gene panel links in oncoprint tooltip Aug 23, 2023
@inodb
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inodb commented Aug 24, 2023

@BasLee Thanks! Tali's proposal looks great! I wonder what happens in the tooltip for this case:

  • a zoomed out oncoprint with e.g. two patients but they have different panels. What would the text say?

@BasLee
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BasLee commented Aug 30, 2023

I wonder what happens in the tooltip for this case:

  • a zoomed out oncoprint with e.g. two patients but they have different panels. What would the text say?

@inodb When rendering the oncoprint tooltip, the profiled and non-profiled gene panels are grouped separately.
So for example, when you have two patients with different gene panels, first the tooltip will list all the gene panels of those two patients that are profiled (plus their count), and after that all gene panels that are unprofiled (with their count). When the patients have different panels, the counts will differ in the tooltip.

image
Example of two patients with one gene panel only present in one of the two patients, and a gene panel that is shared by the patients

@inodb
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inodb commented Aug 30, 2023

@BasLee thanks for investigating! That looks fine to me!

I guess we can merge this then?

@inodb inodb force-pushed the oncoprint-tooltip-non-profiled-panels branch from c9daf2d to 195d4b5 Compare August 30, 2023 14:50
@inodb inodb merged commit 614eac8 into cBioPortal:master Aug 31, 2023
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3 participants