-
Notifications
You must be signed in to change notification settings - Fork 33
Open
Description
Hello,
I am plotting a structure with the following script:
import forgi.graph.bulge_graph as fgb
import forgi.visual.mplotlib as fvm
import matplotlib.pyplot as plt
seq = "AAAACCGGGCCUUUUACCCCAAAUUGGAA"
mfe = "((((..(((..)))..))))...((..))"
bg, = fgb.BulgeGraph.from_fasta_text("".join([">test\n", seq, "\n", mfe]))
fvm.plot_rna(bg, ax=None, offset=(0, 0), text_kwargs={}, backbone_kwargs={'color':'k', 'lw':2}, basepair_kwargs={'color':'black', 'lw':5, 'linestyle':':', 'edgecolor':'black', 'alpha':1}, lighten=0.5)The structure looks just fine, and I can modify the backbone appearance with the keyword arguments passed to matplotlib.
Unfortunately, the basepair just do not show up.
I am playing around with all possible arguments (color, line width, lifestyle, edge color, alpha) to try and have them showing up, but it's not working.
Any help?
Thanks
P.s. I suspect this is because I am not explicitly passing a list of paired nucleotides to be connected, and it is not clear to me how to do that at this moment.
P.p.s. nevermind, bg.to_pair_tuples() shows that the base pairs are correctly captured, so the issue is in the visualization itself.
Metadata
Metadata
Assignees
Labels
No labels