network_plot.py issue

[jinghuazhao]

I have been able to generate network plot with the the older version,

https://data.broadinstitute.org/mpg/depict/documentation.html

but not the GitHub version.

Does anybody have experience setting this up?

[jinghuazhao]

I have figured this out.

Under 1.8.0_131-b11 which we use, I uncomment.

pd.options.mode.chained_assignment = None # default='warn'

as with those associated with the following chunk

if out is None:
out = os.path.join(os.getcwd(), 'network_plot', 'network_plot')
out = os.path.abspath(out) # convert to absolute path.
# e.g. /Users/pascaltimshel/Dropbox/0_Projects/git/DEPICT/src/network_plot/network_plot
elif out == "": # empty string
raise Exception("No output_label label given. Please correct the config file")
else:
out = os.path.abspath(out) # convert to absolute path. # E.g.:
# os.path.abspath(".") --> '/Users/pascaltimshel/Dropbox/0_Projects/git/DEPICT/src'
# os.path.abspath("./SOMEDIR") --> '/Users/pascaltimshel/Dropbox/0_Projects/git/DEPICT/src/SOMEDIR'
# os.path.abspath("SOMEDIR/ANOTHERDIR") --> '/Users/pascaltimshel/Dropbox/0_Projects/git/DEPICT/src/SOMEDIR/ANOTHERDIR'
# os.path.abspath("/Users/pascaltimshel/") --> '/Users/pascaltimshel'

and the the call -S to Cytoscape 3.6.0 require absolute path.