R visualization package : Genome-wide distribution and orientation of translocations

Question

[Bastien Hervé]

Hello,

Any ideas how to create a genome-wide visualization like this one, from this publication ?

I read the M&M and the Extended Protocol Procedures but they just mention R language...

I contacted the first author but did not get an answer yet...

This is a genome-wide representation of translocation events, with a bin size of 5 million bases, one event in a bin is a black dot, 5 events in a bin is a red dot etc...

I tried to use chromPlot and it works well, I got histograms of events. It's cool but I do have like 500 events on the same bin and casual events randomly that I can barely see due to the 500 events...

I'm interested in the events count aggregation using dots which I can not find yet over the R packages...

Thanks !

[Pierre Lindenbaum]

any raw /plain text data available ?

[Bastien Hervé]

Authors did not shared fastq files of theirs experiments. Futhermore, to get the translocation visualization like above, they used LAM-HTGTS technique and they did not mention all parameters and filters in the publication. Sadly, I can't share my data here, it is not public yet. But I got a GRanges structure in which each line is a translocation junction (one black point).

[Pierre Lindenbaum]

I'm interested in the events count aggregation using dots which I can not find yet over the R packages...

bedtools https://bedtools.readthedocs.io/en/latest/content/tools/groupby.html ?

[Bastien Hervé]

Thanks Pierre, but I'm interested in the dots visualization not in the count aggregation step

[Nicolas Rosewick]

Try to contact the author of the publication for the source code of this plot.

[Bastien Hervé]

I contacted the first author but did not get an answer yet...

I have contacted first, second authors and an other one in the middle of the author list but I got no answer... (1 month ago)