plot a bedgraph
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4.2 years ago
sacha ★ 2.3k

Hi ,

I would like to plot a bed file with numeric values ( = bedgraph). My input data are : chr pos start end value ( value between -1 and 1)

exemple :

chr19   50906809        50907015          0.8173737057494912
chr19   50909381        50909562          0.2639404477044525
chr19   50909499        50909702          0.5421707627971464
chr19   50909697        50909863          0.7663584319162735


I would like something like this :

Do you have an easy way ? R package or matplotlib solution ?

bed bedgraph plot RNA-Seq • 5.6k views
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Maybe something interesting in : https://bernatgel.github.io/karyoploter_tutorial/

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Haven't tried, maybe something in https://github.com/deeptools/pyGenomeTracks

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Python !! This is awesome ! Thanks !

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pyGenomeTracks can't plot multiple chromosomes at once

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4.2 years ago
sacha ★ 2.3k

I just discovered the Sushi package which do the job pretty well !
https://bioconductor.org/packages/release/bioc/html/Sushi.html
See plotbedgraph

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Hi there, the plot you have in your original post has the whole genome and uses points intead of bars. Would this possible to do in Sushi? I went through the pdf manual but I could not find the exact usage. Best

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4.2 years ago

qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots

https://www.biorxiv.org/content/early/2014/05/14/005165

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Thanks pierre. I will try. I forgot to mention that my bed refer to amplicon.

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yeah but for ~100bp will you really be able to see a width of a scaled interval ? should be <1 pixel for a human genome.