plot a bedgraph

Question

[sacha]

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 ?

[Bastien Hervé]

Maybe something interesting in : https://bernatgel.github.io/karyoploter_tutorial/

[WouterDeCoster]

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

[sacha]

Python !! This is awesome ! Thanks !

[860101959]

pyGenomeTracks can't plot multiple chromosomes at once

Answer 1

[sacha]

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

[sm.hashemin]

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

Answer 2

[Pierre Lindenbaum]

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

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

[sacha]

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

[Pierre Lindenbaum]

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.