Plotting specific coordinates from a gff3 file

[soungalo]

Suppose I have a gff3 file and I want to plot everything on chr1 positions 1000-2000.
Can you please provide some example code? Should I use the BiopythonTranslator class? How exactly? (maybe there should be an example in the documentation).
Thanks!

[veghp]

Hi, thanks for trying this package out. I think your question has been answered in #34 (comment).

Specifically, you can plot only a section of the record (from start to end):

start = 1000
end = 2000
record = BiopythonTranslator().translate_record(gff_records[0][start:end])
ax, _ = record.plot(figure_width=10, strand_in_label_threshold=7)

see the other thread for details, and please let me know if that solves the problem.

[APengs494]

How to use GraphicFeature to change gene color from gff3 files.

[veghp]

Define your biopython translator with a custom set of colours, as described in the documentation: https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer#custom-biopython-translators

then you can use it to read your gff file and plot it.