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CNA figure

Hi. I am interested in creating a figure like figure 2b here https://ashpublications.org/view-large/figure/7519999/1362f2.jpeg Figure 2 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!

python figure plot r cna
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updated by Kevin Blighe Kevin Blighe • written by ehruan • ehruan

2 answers

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

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written by 2nelly 2nelly

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.

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written by Kevin Blighe Kevin Blighe

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

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written by 2nelly 2nelly

Thanks - I was evidently working too late again.

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written by Kevin Blighe Kevin Blighe

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