Note
Go to the end to download the full example code
6.2. Possible ConversionΒΆ
Plot directed graph of possible conversion
from bioconvert.core.graph import create_graph
If you use pygraphviz, you can have a good quality image using:
import matplotlib as mpl
mpl.rcParams["figure.dpi"] = 250
In order to create the following image, you need graphviz and pygraphviz. If you cannot install those packages, you may use a singularity image like in the following example by setting the use_singularity parameter to True. This would work under Linux. Not tested on other systems yet.
try:
create_graph("conversion.png", use_singularity=True)
except:
create_graph("conversion.png", use_singularity=False)
Creating directory /home/docs/.config/bioconvert
Downloading singularity. Please wait
singularity pull --name /home/docs/.config/bioconvert/graphviz.simg shub://cokelaer/graphviz4all:v1
Warning ! Singularity must be installed if you want to you used it ! Switching to local graphviz executable if available
from pylab import imshow, imread, xticks, yticks, gca
imshow(imread("conversion.png"), interpolation="nearest")
xticks([])
yticks([])
ax = gca()
ax.axis("off")
(-0.5, 2756.5, 634.5, -0.5)
Total running time of the script: ( 0 minutes 1.546 seconds)