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 ...
- 166
8
votes
Accepted
How can I colour boxes in Gviz AnnotationTrack in R?
Did you try the fill argument?
Something like this:
...
- 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")
- 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"))
- 535
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 ...
- 5,060
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.
- 629
1
vote
How can I install bioconductor-gviz and use it in jupyter notebook?
Use BiocManager::install()
...
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 ...
Only top scored, non community-wiki answers of a minimum length are eligible