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plot a bedgraph

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 :

enter image description here

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

bed bedgraph plot rna-seq
• 9,863 views • link
updated by 860101959 • 860101959 • written by sacha sacha

Python !! This is awesome ! Thanks !

• 1 views • link
written by sacha sacha

pyGenomeTracks can't plot multiple chromosomes at once

• 0 views • link
written by 860101959 • 860101959

2 answers

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

• 1 views • link
written by sacha sacha

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

• 1 views • link
written by sm.hashemin sm.hashemin

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

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

enter image description here

• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

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

• 1 views • link
written by sacha sacha

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.

• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

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