Entering edit mode
5 months ago
a.loka92
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0
I run AmpliconArchitect (https://github.com/virajbdeshpande/AmpliconArchitect) and AmpliconClassifier (https://github.com/AmpliconSuite/AmpliconClassifier) to detect extrachromosomal DNA (ecDNA) on a cohort of human samples. Now I would like to make a nice plot showing the reconstructed amplicon, similar to Fig. 1B of this paper: https://www.sciencedirect.com/science/article/pii/S0092867411015169 Any idea/suggestion? Thank you in advance.
the ampliconarchitect readme points to cycleviz https://github.com/AmpliconSuite/CycleViz not exactly the same probably but looks pretty good
yeah, I tried it out but it's not the same, not exactly what I'm looking for..
perhaps can consider emailing the authors. my personal opinion is that I think authors should be much more forthcoming about how figures are generated, including citing relevant software used to create figures or putting bespoke code for it online. people will cite all the tools they used except the things they used to create figures which i think is like creating intentional speedbumps for science. that said, the lead author Tobias Rausch creates interesting visualization tools (e.g. https://github.com/tobiasrausch/wally/), perhaps they would be able to provide some more info on what they used (but technically should email the corresponding authors)
random other aside: figures are somewhat similar also to the PURPLE/GRIDDS/LINX pipeline figs https://github.com/hartwigmedical/hmftools/blob/master/linx/README_VIS.md
Sorry for being late but I didn't notice this thread before. The plots in our 2012 Chromothripsis paper were generated using circos. These scripts should get you started: https://github.com/tobiasrausch/circosplots. As cmdcolin said, I do maintain wally where the 'matches' subcommand is IMHO useful to visualize ecDNA as in this Figure but I don't have yet any circular layout in that tool.