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Gene plot similar to LocusZoom

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.

r visualization
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updated by Ram Ram • written by GabrielMontenegro GabrielMontenegro

1 answer

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

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updated by Ram Ram • written by Sukhi Singh Sukhi Singh

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.

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updated by Ram Ram • written by GabrielMontenegro GabrielMontenegro

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

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written by Sukhi Singh Sukhi Singh

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.

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written by GabrielMontenegro GabrielMontenegro

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