display of chromosomes (on the linear scale) and translocations
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Bogdan ▴ 620
Last seen 14 hours ago
Palo Alto, CA, USA

Dear all,

please would you advise if there is any package in BioC/R that could help with the following data visualization : 

1 -- we have a set of SNV, CNV, SV from cancer samples

2 -- we would like to display the SNV and CNV along the chromosomes (on the linear scale, ie. HORIZONTALLY)

3 -- we would like to display the SV, especially TRANSLOCATIONS, as VERTICAL LINES connecting the breakpoints on the chromosomes that are represented HORIZONTALLY

thank you very much,

-- bogdan





ggviz ggplot2 gviz circlize Rcircos • 481 views
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On the same line of thought,  I believe that I could adapt the functionality of some R packages that display the synteny regions across multiple species (here please see an example Figure 1 from http://www.g3journal.org/content/7/6/1775.figures-only ),

In my case, instead of distinct species, I will just show distinct chromosomes connected by translocations, although I have not found yet a R/BioC package that does this display.  

If anyone has any suggestions, please let me know.

thanks a lot, 

-- bogdan



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