Gene plot similar to LocusZoom

Question

[GabrielMontenegro]

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.

Answer 1

[Sukhi Singh]

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

[GabrielMontenegro]

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.

[Sukhi Singh]

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

[GabrielMontenegro]

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.