Sorting algorithm

[willdurand]

Hi,

I tried to understand how the samples where sorted using http://www.cbioportal.org/oncoprinter.jsp with the default example data but I failed. At first, I thought that was given the natural order of the genes to sort the tracks on Y, and then the samples (on X) were sorted given the natural order of the samples of the first gene. This obviously is not correct.

I found out that we could maybe sort the events alphabetically but this, again, was not correct. I tried to dig into the source code of this lib but I got lost and I don't really find good resources on this. Is there a de facto sorting algorithm for OncoPrint charts? I have read about mutual exclusivity, like here where the "memo sort" is mentioned but this paper talks about something slightly different if I am not mistaken. Given that there has different versions of the OncoPrint, I am not sure where to find the information, hence this issue.

I hope someone could help me figure out how to sort the genes, samples and events as done on the cBioPortal. Thank you for your help.