Question: Gene plot similar to LocusZoom
0
gravatar for GabrielMontenegro
3.2 years ago by
United Kingdom
GabrielMontenegro520 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 • 2.6k views
ADD COMMENTlink modified 3.2 years ago by Sukhdeep Singh9.7k • written 3.2 years ago by GabrielMontenegro520
5
gravatar for Sukhdeep Singh
3.2 years ago by
Sukhdeep Singh9.7k
Netherlands
Sukhdeep Singh9.7k 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 written 3.2 years ago by Sukhdeep Singh9.7k

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 written 3.2 years ago by GabrielMontenegro520

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

ADD REPLYlink written 3.2 years ago by Sukhdeep Singh9.7k

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 3.2 years ago by GabrielMontenegro520
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