Add gene-level charts to study view for categorical molecular profiles

[tmazor]

Background:

• cBioPortal: cBioPortal is an open-source platform for cancer genomics data analysis and visualization. It provides a centralized resource for exploring and analyzing large-scale cancer genomic data sets, including genomic alterations, gene expression, and clinical information. The platform integrates data from multiple sources, including The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC), and makes it available through a web interface for researchers, clinicians, and the general public. Please refer to the cBioPortal home page for an overview.

• Study View: The Study View page of cBioPortal provides users with an interactive view to explore the clinical & genomic data associated with a study. Data is represented as individual charts which can be used to filter to subsets of data.

Currently, the only way to visualize molecular data like mutations, copy number alterations or structural variants in Study View is a summary table showing the frequency of mutations in each gene across all samples:

However, users often want to look at specific genes in greater detail, to understand the exact types of alterations found in specific genes. This can be done by running a query, but we want to support this in Study View as well.

Goal:
For molecular alterations with continuous data values, like gene expression, there is an option to add charts showing the expression of a particular gene across all samples. The goal of this project is to extend that feature to support mutations & structural variants.

The interface to add gene-specific data for continuous profiles already exists:

The menu will need to be expanded to include mutation, copy number and structural variant profiles.

Depending on the type of profile select, a pie chart with the following values should be added to the study view page for each gene:

The slices for mutations (option 1):

• Mutated (the samples with one or more mutations in the gene)
• Not mutated (the samples without mutations in the gene)
• Not profiled (the samples that were not profiled)

The slices for mutations (option 2):

• mutation types (as defined in oncoprint)
• Not mutated (the samples without mutations in the gene)
• Not profiled (the samples that were not profiled)

The slices for mutations (option 3):

• number of mutations in the gene
• Not mutated (the samples without mutations in the gene)
• Not profiled (the samples that were not profiled)

The slices for SVs (option 1):

• Has SVs
• No SVs
• Not profiled

The slices for SVs (option 2):

• SV types
• No SVs
• Not profiled

The slices for SVs (option 3)

• Fusion partner gene (one partner per slice)
• No partner
• No SVs
• Not profiled

Approach:

• Develop new charts in TypeScript that use the existing REST API endpoints to get the pie chart breakdowns
• Enable interactivity in the pie charts

Need skills:
JavaScript

Possible mentors:
@haynescd
@mlizchap

[aditygrg2]

Hi @inodb will love to help in this project.

[vish-han]

@tmazor @inodb Who is the possible mentor for this project, I have some suggestion and ideas that I would like to discuss with the mentor.

[Gazalshyam]

Hello @tmazor @inodb On this project, I would like to talk about some ideas and make some clarifications. Could you please let me know who is the project's mentor?

[saksham28hans]

Hi, I would like to contribute on this project.

[melondotdev]

Hi @tmazor, I'm a former biomedical researcher (highest degree is a Master of Science in Physiology) who is trying to make a career switch to software engineering, and while I do not have much experience in coding, I would love to work on this project with you through the Google Summer of Code program. Please let me know if this opportunity is still available. Thanks, Han.

[inodb]

Thanks for your interest all! Please reach out to @haynescd about any questions related to this project

[Ahmed89shaaban]

Have new idea to collaborate to make good decisions

[heymitali]

Hi, I am Mitali. I am interested to work for the project. Kindly let me know for the opportunities.

[LalitDeore]

Hey,

I am expressing my interest in participating in this project. I have a background in open-source work and have previously contributed to projects. Additionally, I have been accepted into the GitHub Octernship Program under the Shuffle Organization.

My skill set includes proficiency in React.js, and Javascript. Could you kindly provide me with any prerequisites or tasks that I could complete as a demonstration of my abilities and suitability for this project?

Thank you.