CNA figure

Question

[ehruan]

Hi. I am interested in creating a figure like figure 2b here https://ashpublications.org/view-large/figure/7519999/1362f2.jpeg where the chromosomes are on the Y axis and the samples are on the X-axis. How can I align all my cases to the same Y axis chromosome parameters? I am not sure where to start or what this plot is even called but I have the chromosome and location information for each sample. Thank you!

Answer 1

[2nelly]

if you are not familiar with python or R coding, you can easily create something similar with the heatmap function of cnvkit or the cnspec function of R package GeneVisR. See below:

cnvkit

GeneVisR

Answer 2

[Kevin Blighe]

Edit: please ignore. User was referring to Figure 2B, not Figure 2A

+++++

It's called an OncoPrint - see https://jokergoo.github.io/ComplexHeatmap-reference/book/oncoprint.html

See a useful practical example, here: 12.2 The measles vaccine heatmap.

[2nelly]

Sorry Kevin, I think he is talking about the 2B figure not 2A.

[Kevin Blighe]

Thanks - I was evidently working too late again.