Mutation burden plot

[jjgao]

Background:

Different cancers have different mutation burdens. One nice way to visualize them is the so-called hamburger plot. In the figure below as discribed in this paper, "each dot corresponds to a tumour–normal pair, with vertical position indicating the total frequency of somatic mutations in the exome. Tumour types are ordered by their median somatic mutation frequency. The bottom panel shows the relative proportions of the six different possible base-pair substitutions, as indicated in the legend on the left."

Goal: Visualizing mutation burdens in OncoPrint and the study view page of cBioPortal

Approach:

• The three types of data (mutation burdens, Mutation spectrum, and Cancer Type) are already visualized in OncoPrint. E.g. open this link and add the three attributes. If we order by Mutation Count and Mutation spectrum, we kind get a similar plot.

• In order to make it more like the one in the paper, we can:
  • support custom height so we can increase the track height of Mutation Count
  • plot dots instead of lines for Mutation Count
  • add median line
• We can add the plot (without genes) into study view page.

Need skills:

• Javascript
• ReactJS

Possible mentors:

[nilaypathak]

hello sir, I am a web developer and a Data Science Enthusiast from IIT Kharagpur, India. I also have experience in working with ReactJS for the past couple of months. I am interested in the project. Can you please suggest me how to get started. Thank You

[pieterlukasse]

Nice @jjgao :+1: Idea: maybe cancer type should not be the only possible item on the x-axis?

[jjgao]

Moved the issue here. Looks like we pretty much have the feature in oncoprint already. We just need to improve the visualization a little.

[schultzn]

But shouldn't this be a study view feature?

[jjgao]

@schultzn yes, it should be... thinking of reusing oncoprint code there.

[stale[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[stale[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.