Show alteration frequencies for groups in OncoPrints

[inodb]

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.

• OncoPrint: The OncoPrint is a heatmap-like chart that shows what genomic alterations are present in a cohort. It is one of the most popular visualizations in cBioPortal.

  

  In the figure above the OncoPrint shows one column per patient and one row for each gene (KRAS/NRAS/BRAF). Each glyph shows you what type of alteration is happening in that specific patient's tumor. The example here shows a cohort of colorectal cancer patients and it is noticeable that the mutations are mutually exclusive across the KRAS, NRAS and BRAF genes. You can interactively explore this example here.

• Project: OncoPrints currently support the visual separation of groups, as defined by clinical data elements in annotation tracks (via the "Show gaps" option in the Annotation track menu), see this example: https://bit.ly/3IaS8YZ

  A missing feature is to indicate the alteration frequencies of the individual groups, like in this example from Chatila et al.:

  

Goal: Show alteration frequencies per group

Approach: We could add a new menu item in the settings menu for the track, e.g.: "Show alteration frequencies of each group"

Need skills:

• JavaScript, React

Possible mentors: @inodb @gblaih @alisman

[Abinash-bit]

@inodb Hlo I am intrested in solving this issue please guide me.

[singhvaibhav924]

Hey @inodb , I am finding this issue quite interesting as well as challenging can anyone please help me from where to start .....

[kts-desilva]

Hi @inodb , I am interested in solving this issue as a frequent user of cbioPortal. Please guide me on the steps to start.

[eshan-003]

Hi @inodb , i am well versed in MERN stack and web dev in general . I came across this project and feel that i can contribute to this.Plz guide me on the steps to start

[Ruthu364]

Hi @inodb ,i am interested in this project.plds guide me to start

[hendsaeedd]

Hi @inodb ,i am interested in this project.

[sawaisinghh]

Hi @inodb, I know this tech stack very well. So, I feel like i can solve this issue.

[Danish-Belal]

Hello @inodb can i work on this issue ? Kindly assign to me.

[Sudesha-STR]

Hello @inodb, I am finding this issue quite interesting. Can you please assign it to me?

[farmannaseem]

Hi! Can I Work on this issue ? IF Yes Then Assign me This Issue Thank you!! :)

[inodb]

Hi all - please take at running the frontend: https://github.com/cBioPortal/cbioportal-frontend. Feel free to reach out on slack for further questions

[gaurab-khanal]

Hi all - please take at running the frontend: https://github.com/cBioPortal/cbioportal-frontend. Feel free to reach out on slack for further questions

I can't get invitation for slack. Can you sent me? email - khanalgaurab98@gmail.com

[inodb]

@gaurab-khanal it looks like you're already part of the workspace. Are you able to log in on https://cbioportal-public.slack.com?

[gaurab-khanal]

@gaurab-khanal it looks like you're already part of the workspace. Are you able to log in on https://cbioportal-public.slack.com?

Yes I did.

[SohilP25]

Hello, I would like to contribute to this issue can you please guide me?

[HarounTheGreat]

Greetings, I'd want to contribute to this problem. Would you kindly direct me?

[OmkarBorker]

Hello @inodb i am interested in this issue and would like to contribute to this issue.Kindly direct me?

[seifbhxc65]

hi @inodb how can i be part of the slack portal?

[inodb]

@seifbhxc65 you can sign up at slack.cbioportal.org

[alisman]

Move to https://github.com/cBioPortal/cbioportal/issues/10295