Plot reads from .BAM file above reference sequence in R?
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7.1 years ago
stianlagstad ★ 1.1k

I want to plot something like this:

enter image description here

This was produced with Gviz. My problem with Gviz is the empty space added at the bottom of the plot (below the reads). I posted a question about that here.

Do you have any suggestions on how I can plot reads aligned to a reference sequence in R, and not use Gviz?

Edit: The observant might have noticed that the "empty space problem" with the Gviz plot was solved in the post I linked to. I'm still curious if there are other solutions, though.

R plot • 4.6k views
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I surmise it might be easier to do it manually in inkscape or gimp or semi-manually with imagemagick convert. Surely it is possible in pure R but it might be a pain... (I'd be happy to be proved wrong though...)

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Thank you for the answer! For a single case it would be easier to do it manually, but I have to do this automatically in R :) I have a solution that works with Gviz, but that empty space is giving me problems when I export the plot in scalable formats.

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Try Sushi: An R/Bioconductor package for visualizing genomic data or if you export pdf via gviz, and import in Adobe Illustrator, each feature becomes an object and you can manually edit it.

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Thank you for the answer! I have looked at the Sushi manual before but I couldn't see anything that would help me. Could you point me in the right direction?

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I haven't used Sushi personally, I suggested as it might be useful. I could suggest you a few more, that I've come across, might solve your purpose.

First of all this a resource of most tools What Tools/Libraries Do You Use To Visualize Genomic Feature Data?

ggbio - has support for BAM file. GenomeGraphs

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Thank you, but rest assured that I've done more than a few searches and I've looked at more than a couple of packages before coming here to ask the question. If you have a specific suggestion that would be helpful :)

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Just for the time being, if you want you can use the illustrator trick, if you export the pdf plot from Gviz. Good Luck!

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