search

gregversteeg / bio_corex

A flexible version of CorEx developed for bio-data challenges that handles missing data, continuous/discrete variables, multi-CPU, overlapping structure, and includes visualizations
Apache License 2.0
139 stars 29 forks source link

Error in Centos 7? #13

Closed prasanna224 closed 5 years ago

prasanna224 commented 5 years ago

While running a randomly sampled file with around 40k rows where a few lines are given below in Centos 7 machine with the command below:

python3 vis_corex.py /home/usr1/dx_eighth.csv --delimiter="|" --layers=16,8,1 --dim_hidden=3 --missing=-1e6 -c -b -v -o dx_sub --ram=72 --cpu=36

I am getting the following output in the end:

TC at layer 1 is: 0.070 TC at layer 2 is: 0.346 Groups in sorted_groups.txt Pairwise plots among high TC variables in "relationships" vis_corex.py:174: FutureWarning: arrays to stack must be passed as a "sequence" type such as list or tuple. Support for non-sequence iterables such as generators is deprecated as of NumPy 1.16 and will raise an error in the future. all_edges = np.hstack(map(np.ravel, weights)) weight threshold is 0.000000 for graph with max of 100.000000 edges non-isolated nodes,edges 65 99 Error: remove_overlap: Graphviz not built with triangulation library Error: remove_overlap: Graphviz not built with triangulation library non-isolated nodes,edges 65 64 Error: remove_overlap: Graphviz not built with triangulation library Error: remove_overlap: Graphviz not built with triangulation library

Is this expected behavior as the pdf files generated inside graphs folder inside the output folder appear to be errorneous and unclean?

Sample file:

DX101|DX110|DX115|DX118|DX142|DX143|DX155|DX160|DX166|DX169|DX175|DX184|DX196|DX212|DX215|DX218|DX222|DX223|DX234|DX235|DX239|DX253|DX254|DX267|DX271|DX275|DX277|DX278|DX279|DX295|DX298|DX310|DX315|DX332|DX335|DX342|DX343|DX344|DX356|DX385|DX386|DX399|DX404 8|0|1|6|0|0|0|0|0|0|0|0|5|0|3|0|0|6|0|453|0|0|0|2|0|0|6|0|0|0|9|4|6|0|0|1|1|0|9|0|0|41|81 0|4|0|0|0|4|1|0|53|0|0|2|0|0|1|0|0|0|0|0|0|4|0|0|0|0|3|0|0|0|0|0|11|0|4|0|0|0|0|0|7|0|0 0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0 0|0|0|0|1|0|0|0|0|0|0|0|0|0|9|0|0|3|0|0|0|0|0|0|0|0|0|2|0|0|2|0|25|0|0|0|0|0|0|0|2|0|0 ......... ......

gregversteeg commented 5 years ago

vis_corex outputs a .dot file which is a network format for graphviz. Then it calls graphviz to compile a PDF image from the .dot file. Unfortunately, getting graphviz installed correctly is difficult, with platform specific issues. Please look at the new "troubleshooting graphviz" section of the readme to see if those steps help. You can try to manually run the graphviz compiling utility using statements like the one listed in the readme "sfdp tree.dot -Tpdf -Earrowhead=none -Nfontsize=12 -GK=2 -Gmaxiter=1000 -Goverlap=False -Gpack=True -Gpackmode=clust -Gsep=0.02 -Gratio=0.7 -Gsplines=True -o nice.pdf"

prasanna224 commented 5 years ago

Thanks for your quick response. I have tried almost all possibilities but a nice output without error seems most elusive for CentOS 7.