igraph2image FileNotFoundError

[yzongy]

Hi, I was running:

igraph = primes2igraph(primes)
igraph2image(igraph, "test_simpleModel.pdf")

and got this error:

INFO created None Traceback (most recent call last): File "/Users/yzongy/BooleanNetworks/test.py", line 21, in igraph2image(igraph, "test_simpleModel.pdf") File "/Users/yzongy/.pyenv/versions/3.9.7/lib/python3.9/site-packages/pyboolnet/interaction_graphs.py", line 213, in igraph2image digraph2image(igraph, fname_image, layout_engine=layout_engine) File "/Users/yzongy/.pyenv/versions/3.9.7/lib/python3.9/site-packages/pyboolnet/digraphs.py", line 274, in digraph2image proc = subprocess.Popen(cmd, stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.PIPE) File "/Users/yzongy/.pyenv/versions/3.9.7/lib/python3.9/subprocess.py", line 951, in init self._execute_child(args, executable, preexec_fn, close_fds, File "/Users/yzongy/.pyenv/versions/3.9.7/lib/python3.9/subprocess.py", line 1821, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename) FileNotFoundError: [Errno 2] No such file or directory: '/usr/bin/fdp'

I would be very grateful if you could guide me through it.

Best,

Bill

[hklarner]

Hi Bill,

looks like you don't have Graphviz installed. You are on Windows, right?

• https://pyboolnet.readthedocs.io/en/master/installation.html#graphviz

[yzongy]

Hi,

Thanks for your quick reply. I am on Mac and have installed graphviz 2.50.0

[hklarner]

The command /usr/bin/fdp is missing. fdp is the default layout engine. What happens when you call fdp in the terminal? What happens when you call dot in the terminal? What happens when you change the layout engine to dot?

igraph2image(igraph, "test_simpleModel.pdf", layout_engine="dot")

[yzongy]

Hi Hannes,

I tried all engines one by one but still not working.

Are there any other approaches for visualisation?

Best,

Bill

[hklarner]

What happens when you type dot in the terminal?

[yzongy]

Hi Hannes,

It did work when fdp or dot was called in the terminal, which printed XML file from a dot file: $ fdp -Tsvg irma.dot

[hklarner]

Right. So you can use pyboolnet to create the dot file and then call fdp or dot yourself from the command line.

If you want to create the pdf from pyboolnet you need to find out the path for the layout engines e.g. fdp and dot and make changes to the settings.cfg file.

Find out the path to your layout engines by calling $which fdp or $whereis fdp.

The settings.cfg file is in the pyboolnet directory on your computer. You can find out where you have pyboolnet installed by importing pyboolnet and calling .__file__ on it:

$ python3
>>> import pyboolnet
>>> pyboolnet.__file__
~/lib/python3.8/site-packages/pyboolnet

The settings file will then be located in

• ~/lib/python3.8/site-packages/pyboolnet/binaries/settings.cfg

[yzongy]

It works! Thanks for your time and step by step guidance!

Best,

Bill

[hklarner]

Great. Let me know if anything else comes up.