Question: Gene plot similar to LocusZoom
0
gravatar for GabrielMontenegro
4.1 years ago by
United Kingdom
GabrielMontenegro540 wrote:

After doing some analysis I am interested in some particular regions of the genomes and was interested to see which genes were there.

I wanted to know if there was some easy way, that would let me plot the genes in R in similar way that LocusZoom does. I tried downloading the LocusZoom source code but simply could not figure out how the gene plotting was done.

 

visualization R • 3.3k views
ADD COMMENTlink modified 4.1 years ago by Sukhdeep Singh10.0k • written 4.1 years ago by GabrielMontenegro540
5
gravatar for Sukhdeep Singh
4.1 years ago by
Sukhdeep Singh10.0k
Netherlands
Sukhdeep Singh10.0k wrote:

Check this out Plotting Read Densities And Gene Tracks In R?

Also, a new addition to that is Sushi: An R/Bioconductor package for visualizing genomic data

ADD COMMENTlink modified 7 weeks ago by RamRS25k • written 4.1 years ago by Sukhdeep Singh10.0k

Thanks! Have you used the Sushi package before? I'm trying to plot a simple genomic region but keep getting an error. I'm trying the plotGenes function.

ADD REPLYlink modified 7 weeks ago by RamRS25k • written 4.1 years ago by GabrielMontenegro540

I don't get any error. I just used the example from the ?plotGenes function. What error is that?

ADD REPLYlink written 4.1 years ago by Sukhdeep Singh10.0k

I downloaded a bed file from the ensembl website for my build. When I run the plotGenes function I just get a "yes" printed on the console, it never plots anything and I just have to stop it.

ADD REPLYlink written 4.1 years ago by GabrielMontenegro540
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 840 users visited in the last hour