Display of oncoplot seems to have a bug

[Vosmeijer, Ilse]

Dear reader,

 

I have been using cbioportal for a while now and the OncoPrinter has been of great help to display my data, however with my current input the oncoplot seems to have bugged. I don’t know what to do about it. If I download the oncoplot it also whites out an entire streak of mutations like it does in the clinical data shown in the screenshot.

What can I do to fix this?

 

 

Kind regards,

Ilse Vosmeijer BSc

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[Pieter Lukasse]

Hi Ilse,

Is this something you can reproduce on cbioportal.org? If yes, could you please share the link to the case where this happens? 

To clarify on the issue: is the problem only with NSMP1033? Did you check this sample in the patient view and is it empty there as well?

Thanks,

Pieter

https://se4.bio 

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[Pieter Lukasse]

Hi Ilse,

Can you please highlight on the figure which parts exactly you mean? 

Thanks,

Pieter

On Thu, Apr 3, 2025 at 8:01 AM Vosmeijer, Ilse <Ilse.Vo...@radboudumc.nl> wrote:

Hi Pieter,

 

I made this oncoplot using cbioportal.org and I used my own data.

It is not so much the whited-out areas, I can fix that manually. It is the stripes that run through the molecular data boxes.

I do not understand what caused it.

 

Ilse

 

Van: Pieter Lukasse <pie...@se4.bio>
Verzonden: woensdag 2 april 2025 16:38
Aan: Vosmeijer, Ilse <Ilse.Vo...@radboudumc.nl>
CC: cbiop...@googlegroups.com
Onderwerp: Re: [cbioportal] Display of oncoplot seems to have a bug

 

Hi Ilse,

 

Is this something you can reproduce on cbioportal.org? If yes, could you please share the link to the case where this happens? 

 

To clarify on the issue: is the problem only with NSMP1033? Did you check this sample in the patient view and is it empty there as well?

Thanks,

 

Pieter

https://se4.bio 

 

 

On Wed, Apr 2, 2025 at 2:23 PM 'Vosmeijer, Ilse' via cBioPortal for Cancer Genomics Discussion Group <cbiop...@googlegroups.com> wrote:

Dear reader,

 

I have been using cbioportal for a while now and the OncoPrinter has been of great help to display my data, however with my current input the oncoplot seems to have bugged. I don’t know what to do about it. If I download the oncoplot it also whites out an entire streak of mutations like it does in the clinical data shown in the screenshot.

What can I do to fix this?

 

 

Kind regards,

Ilse Vosmeijer BSc

De informatie in dit bericht is uitsluitend bestemd voor de geadresseerde. Aan dit bericht en de bijlagen kunnen geen rechten worden ontleend. Heeft u deze e-mail onbedoeld ontvangen? Dan verzoeken wij u het te vernietigen en de afzender te informeren. Openbaar maken, kopiëren en verspreiden van deze e-mail of informatie uit deze e-mail is alleen toegestaan met voorafgaande schriftelijke toestemming van de afzender. Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 80262783.

The content of this message is intended solely for the addressee. No rights can be derived from this message or its attachments. If you are not the intended recipient, we kindly request you to delete the message and inform the sender. It is strictly prohibited to disclose, copy or distribute this email or the information inside it, without a written consent from the sender. Radboud university medical center is registered with the Dutch Chamber of Commerce trade register with number 80262783.

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[Pieter Lukasse]

Thanks, I see. That is strange indeed. Are you able to reproduce this on cbioportal.org without any of your custom data? If yes, can you please share the steps? 
I just tried on a regular oncoprint there and I'm not able to reproduce it. Your steps should help us narrow down on what part of the code could be responsible for this.

Thanks,

Pieter

On Thu, Apr 3, 2025 at 11:47 AM Vosmeijer, Ilse <Ilse.Vo...@radboudumc.nl> wrote:

Hi Pieter,

 

The lines that fade out at the end.

 

Kind regards,

[Pieter Lukasse]

Ok, I can relay this to the frontend team. Maybe you can add more details like which browser (and version) you are using? Or does this happen in all your browsers (e.g. Chrome, firefox, edge)?

Thanks,

Pieter

On Thu, Apr 3, 2025 at 12:11 PM Vosmeijer, Ilse <Ilse.Vo...@radboudumc.nl> wrote:

Hi Pieter,

 

I have only worked with my own custom data so I honestly have no clue how to do it without it.

I noticed that when I load my molecular data separately it does not display this problem and it is only when I add the clinical input, the issue arises.

[Pieter Lukasse]

Thanks for the details. I tried a big oncoprint in Edge as well, but it looks fine on my side (see screenshot). Maybe you have browser plugins that could be affecting how this is rendered? 

Best,

Pieter

On Thu, Apr 3, 2025 at 12:19 PM Vosmeijer, Ilse <Ilse.Vo...@radboudumc.nl> wrote:

Hi Pieter,

 

I can only use Edge.

I am using v.6.1.0

 

Thanks,