Question: plot a bedgraph
1
gravatar for sacha
10 months ago by
sacha1.6k
France
sacha1.6k wrote:

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 ?

plot rna-seq bedgraph bed • 1.1k views
ADD COMMENTlink modified 10 months ago • written 10 months ago by sacha1.6k
2

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

ADD REPLYlink written 10 months ago by Bastien Hervé3.3k
1

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

ADD REPLYlink written 10 months ago by WouterDeCoster36k

Python !! This is awesome ! Thanks !

ADD REPLYlink written 10 months ago by sacha1.6k
1
gravatar for sacha
10 months ago by
sacha1.6k
France
sacha1.6k wrote:

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

ADD COMMENTlink modified 10 months ago • written 10 months ago by sacha1.6k

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

ADD REPLYlink written 16 days ago by sm.hashemin60
0
gravatar for Pierre Lindenbaum
10 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum116k wrote:

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

ADD COMMENTlink modified 10 months ago • written 10 months ago by Pierre Lindenbaum116k

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

ADD REPLYlink written 10 months ago by sacha1.6k

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.

ADD REPLYlink written 10 months ago by Pierre Lindenbaum116k
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