Question: R visualization package : Genome-wide distribution and orientation of translocations
1
gravatar for Bastien Hervé
5 months ago by
Bastien Hervé3.3k
Limoges, CBRS, France
Bastien Hervé3.3k wrote:

Hello,

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

nihms322291f2

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 !

R • 230 views
ADD COMMENTlink modified 3 months ago by Biostar ♦♦ 20 • written 5 months ago by Bastien Hervé3.3k

any raw /plain text data available ?

ADD REPLYlink written 5 months ago by Pierre Lindenbaum116k

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).

ADD REPLYlink written 5 months ago by Bastien Hervé3.3k

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 ?

ADD REPLYlink written 5 months ago by Pierre Lindenbaum116k

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

ADD REPLYlink modified 5 months ago • written 5 months ago by Bastien Hervé3.3k

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

ADD REPLYlink written 3 months ago by Nicolas Rosewick7.3k

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)

ADD REPLYlink written 3 months ago by Bastien Hervé3.3k
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