how to make this plot for mutation?

Question

[mangfu100]

Hi all.

I am wondering that the method of drawing plot like below.

Can it be done automatically by using visualization tools or do I have to write codes and combine all of the bars and tables in the figure using R?

Answer 1

[poisonAlien]

I had same problem, so I made a little R package to plot this kind of plot (generally called oncoplots).

Internally it uses oncoprint script from ComplexHeatmap, but takes care parsing, sorting and format conversion.

[mangfu100]

Thanks you.

The packages you made will be helpful in my research. I will use it later :)

[Zuguang Gu]

If you are using the old script which is shipped with ComplexHeatmap package, be careful there would be some errors when adding annotations (barplot) on rows and columns. (e.g. Errors will occur when there is only one mutation type in the matrix). In the newest version of ComplexHeatmap (available at Github), I added a real oncoPrint() function which wraps the code in the old script but with some improvement. There is also a vignette giving a brief introduction of this new function.

[poisonAlien]

Thanks for the heads up! I will definitely look into it.

[Wenhu_Cao]

Hi, I wonder if the maftools could make oncoplot including both scna and mutation data? Thx!