module for generating circos plot for contigs
fmalmeida opened this issue · 9 comments
The proposition is to generate a circos plot and config file per contig so users can further customize it while already having high-quality figures.
The circos plots must be per-contig and must encode all the specialized and generic annotated features.
It must be something to plot the genomic contexts of the annotation. While in JBrowse users have an interactive tool, this would provide an static manner of seeing the same.
🚀
Under development in dev.
For it to work seamlessly and allow easily summarization or downstream work of results, I need to first implement the 'annotation summary in json' which is available in on my python scripts package: https://github.com/fmalmeida/pythonScripts/blob/master/falmeida_py/bacannot2json.py
Maybe some adjusts on the script will be required so it is able to generate sample for one sample only on demand, and allowing final path to be given as string parameter. Currently, the script is working on finalised runs, containing one or more results.
Added module to generate JSON summary.
now first version of circos plots can be finalised
To make a release:
generate core of circos with mgcplotter and add the virulence and resistance labels to it
Unfortunately mgcplotter will not work as desired because it contatenates the contigs, so should stick to previous plan.
script is ready
add the module in the weekend so it is ready for release.
Module added,
Only three things are now required for release:
- add plots per-contigs as well
- make sure that
rRNAandtRNAare also plotted - update docs
Circos properly generated:
Think plotting all contigs alone will be for next release as users can easily adjust the circos.conf file to plot only desired contig and run circos on new conf.