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perslab / depict

DEPICT code, instructions and an example
GNU General Public License v3.0
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network_plot.py issue #10

Closed jinghuazhao closed 6 years ago

jinghuazhao commented 6 years ago

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 commented 6 years ago

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.