12 votes
Accepted

How to make chromosome color maps for bed ranges

You can use karyoploteR to plot your regions on an ideogram quite easily. Disclosure: I'm one of the authors of the tool. For this example I'll start creating 4 GRanges with random regions, but with ...
bernatgel's user avatar
  • 166
8 votes
Accepted

How can I colour boxes in Gviz AnnotationTrack in R?

Did you try the fill argument? Something like this: ...
benn's user avatar
  • 3,571
4 votes

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

# Install the BiocManager package first install.packages("BiocManager") library("BiocManager") # Then install the Gviz package BiocManager::install("Gviz")
Aedin's user avatar
  • 156
3 votes
Accepted

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

Did you try following the installation instructions? Try this in R: source("https://bioconductor.org/biocLite.R") BiocInstaller::biocLite(c("Gviz"))
Jared Andrews's user avatar
2 votes

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

I am not familiar with Gviz, but I am familiar with a variety of tools for visualizing genome features. At the scale of entire microbial genomes, the primary sequence itself is an overwhelming amount ...
Daniel Standage's user avatar
1 vote

Easy way to create gene plot in gviz?

If Python is an option, you could check BioPython and GenomDiagram. This should get the job done.
Mr_Z's user avatar
  • 629
1 vote

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

Use BiocManager::install() ...
Alex Yahiaoui Martinez's user avatar
1 vote
Accepted

How to plot circular chromosomes with Gviz?

The primary author of Gviz confirmed to me via email that this is not possible: Gviz will only give you the traditional linear tracks. There are a bunch of solutions available for visualizing ...

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