Lollipop plot in Group Comparison

[inodb]

Background:

The cBioPortal is an open-access, open-source resource for interactive exploration of multidimensional cancer genomics data sets, which are collected from a multitude of sources such as published research papers, publicly available data repositories, and private data sets. Please refer to the cBioPortal home page for an overview.

The Group Comparison Page makes it easy to make comparisons between groups of tumor samples, such as which gene is more frequently mutated in one set of samples versus another set of samples (see below).

Although it is easy to identify in this view which genes have different mutation frequencies between groups of samples, it is not immediately clear how the specific mutations for these genes are different between the groups. Visualizing these differences can be accomplished with an existing visualization (React component) in the cBioPortal called a Lollipop Plot.

Lollipop Plots are a simple, yet effective, method of visualizing mutations across a gene for a given cohort. Mutation sites are indicated by "lollipops" of varying heights and colors. The heights correspond to the number of mutations at that site and the colors correspond to specific types of mutations.

Figure 1. Lollipop Plot of gene TP53 for study MSK-IMPACT 2017. "Lollipops" are shown across the gene for the various sites of mutation for this study. The heights of the "lollipops" correspond to the number of mutations found at that site for this cohort and the types of mutations are indicated by the colors (see legend on right for reference).

In the Group Comparison Page, the Lollipop Plot should show mutations from one group at the top and mutations from the other group at the bottom. An example mockup is shown below.

Figure 2. Example mockup of what the Lollipop Plot should look like for the Group Comparison Page. Design 1 Design 2

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Goal:

Add the Lollipop Plot visualization to the Group Comparison Page.

Approach:

• Add new tab "Mutations" to the comparison page

• Add the Lollipop Plot React component

• Bonus: Show a Lollipop Plot for more than 2 groups. Instead of showing a full Lollipop Plot on the top and the bottom, we can show circles in a single line where the size of the circle reflects the number of mutations.

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Needed skills:

• React, JavaScript
• Good general programming skills

Possible mentors:

@onursumer @leexgh @fahimehmirhaj

[amanag25]

hey @inodb @ao508 I have some experience with react, javascript and java and would like to contribute to this project for GSOC 2022. Can you provide me some guidance about the process and for getting started?

[tanishq67]

Hi @onursumer @leexgh, I am Tanishq Gupta, a 3rd-year UnderGraduate pursuing Biological Sciences and Bio-Engineering from IIT Kanpur. I completed GSOC’21 under Open Bioinformatics Foundation. I have been programming since, the last 2 years, and I am very much passionate about working on projects that are related to biology. As a web-head, I with my team created this https://www.ppociitk.in/ website in react for our PPOC club from scratch.

I think, I have all the relevant skills to work on this project. Here, is my Resume for reference https://drive.google.com/file/d/1sMQU0juB2xShgKLDDQ8lqcHlJuSemvvO/view?usp=sharing I am really interested in contributing to this project for this GSoC’22. Could you please let me know if there is any sub-issue that I can first fix and put up a PR on to show my competence, or shall I start working on the proposal?

PS:- The given link cBioPortal is not working.

[tanishq67]

@inodb is this issue still up for GSoC?

[ao508]

@tanishq67 this project is still up for GSoC as well :)

[MoatazNasr]

@inodb @ao508 Hey are there any issues to work on before submitting the proposal ?

[ao508]

@MoatazNasr Feel free to begin working on the proposal! There aren't any outstanding issues related to the lollipop plot at this time.

[NehaAr]

Hi i am a PHD student for Data Visualiation in Medical Biochemistry Domain. I work on a lot of expressive plots for detecting cancers in various tissues. I found this plot quite interesting and want to participate in GSOC 2023 to work on this project. I have been a software engineer , prior to my PHD and have skills in javascript , java , python and R

[NehaAr]

Please suggest me if this project would till be up in GSOC 2023

[inodb]

The multiple groups implementation of this project hasn't been done yet. We could file that for GSoC 2023

[harsh2929]

@inodb Is this issue included in GSOC-23, i would love to contribute so kindly please let me know.