Questions tagged [gviz]

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How to order grouped elements in Gviz

Gviz is useful for visualization of gene transcripts by genomic coordinates. I'm using it to show the difference between splice variant transcripts. However, it seems that the ordering of transcript ...
3
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1answer
151 views

How to plot genomic.fna fasta file in R using Gviz?

I downloaded the genome of Staph aureus as DNA sequence from NCBI. I would like to visualize it using Gviz. Is Gviz the right tool to visualize genomes? What are the necessary steps from the sequence ...
1
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3answers
243 views

How can I install bioconductor-gviz and use it in jupyter notebook?

I tried to install gviz in a conda environment, but that library seems to be incompatible to python and r. I tried to setup a clean environment using ...
2
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1answer
121 views

How to plot circular chromosomes with Gviz?

I am using Gviz to plot several tracks. I create a GenomeAxisTrack() and then several AnnotationTrack()s that I feed to ...
5
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1answer
831 views

How to make chromosome color maps for bed ranges

I have genomic .bed file data of 4 different types; type A,B,C,D. These are some examples- Type A: 1 101380000 101710000 A 1 110085000 110320000 A ...
7
votes
1answer
487 views

How can I colour boxes in Gviz AnnotationTrack in R?

I'm learning the Gviz bioconductor package, I generate a plot as follows: ...