Add Variant Allele Frequency Heatmap in Oncoprint - GSoC'25

[rishisulakhe]

Registered "Variant Allele Frequency" as a new type of molecular profile heatmap that the OncoPrint can display. This allowed it to appear as a selectable option in the "Heatmap" of "Track" menu alongside existing heatmaps.

Screen.Recording.2025-11-12.232916.mp4

Preview link: https://deploy-preview-5237.preview.cbioportal.org/

[onursumer]

The functionality looks good, thanks!

The code can be improved/simplified further. See the comments.

[inodb]

Hey @rishisulakhe - this is cool! I tried it, but ran into this issue, everything shows up blank:

[rishisulakhe]

Hi @inodb
Thankyou for review. That issue is now fixed.
You can review it again and let me know if there are any other changes or improvements you'd recommend?

[onursumer]

Almost there. Requested a few more minor changes.

[onursumer]

Hardcoding Variant Allele Frequency might be problematic in the future if we want to add a new mutation related track other than VAF. Not sure what's the best way to address this issue though.

[inodb]

@rishisulakhe Great work! Thank you!

Did some product testing:

Bug 1

For This URL

Maybe don't show VAF as an option in the heatmap when there is no allele frequency available for any of the samples?

Bug 2

Ensure the VAF heatmap reflects OQL, i.e. the EGFR MUT=L858R filter should be applied to the VAF Heatmap track too:

Bug 3

Profiled but EGFR mutation not detected should be white (the line should only show up for the "not profiled" cases, same as for regular mutations track):

[rishisulakhe]

Hi @inodb @onursumer
Some updates.

Bug 1

For [This URL](https://deploy-preview-5237.preview.cbioportal.org/results?

Done✅. Now we are not showing VAF in heatmap option when no VAF data is available for any sample.

Bug 2

Ensure the VAF heatmap reflects OQL, i.e. the EGFR MUT=L858R filter should be applied to the VAF Heatmap track too:

Still working on it.

Bug 3

Profiled but EGFR mutation not detected should be white (the line should only show up for the "not profiled" cases, same as for regular mutations track):

Done✅. Now we are showing light grey color for samples with profiled but not mutated. Here is demo

Also we have one more bug from product team, still need to be address. Like we add clinical track(cancer type) and click on show gaps with %, then add VAF or any heatmap results showing incorrect rendering of genetic track.

[jjgao]

Cool. One comment: The cluster function does not seem to work. cluster example for expression

[tmazor]

This is awesome! A few things I noticed:

1. For other tracks eg RNA, the label in OncoPrint matches the label in the Heatmap dropdown. But for VAF, the OncoPrint is labeled very generically with just 'Mutations':

Let's call the OncoPrint section 'Variant Allele Frequency' instead of 'Mutations'

2. I think this bug is specific to studies with gene panels. Run a multi-gene query. Add VAF heatmap. Delete a gene from the query. If the study does not have gene panels, the deleted gene is still there w/ VAFs -- this matches how RNA/protein heatmaps behave, so this is reasonable. But if I delete the gene in a study that has gene panels, then the VAF track remains but it changes to all 'not sequenced':
   https://deploy-preview-5237.preview.cbioportal.org/results/oncoprint?cancer_study_list=chol_msk_2018&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Ccna&case_set_id=chol_msk_2018_cnaseq&gene_list=IDH1&geneset_list=%20&tab_index=tab_visualize&Action=Submit&heatmap_track_groups=chol_msk_2018_mutations%2CIDH1%2CTP53

3. Maybe a toggle to respect or ignore OQL? Because I can come up with use cases for both sides of this, so maybe we just let the user decide?

[jjgao]

Great points, Tali. @rishisulakhe For point 3, I think it'd be great if we can have a toggle in the VAF heatmap section to let the user decide whether the VAF heatmap should only display VAFs for the mutations shown in OncoPrint above.

[jjgao]

In the menu dropdown, maybe change "Variant Allele Frequency" to "Variant Allele Frequency in Selected Mutations Profile"