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gregversteeg avatar gregversteeg commented on May 26, 2024

Sorry, I put some instructions for this on the bio_corex page: https://github.com/gregversteeg/bio_corex

For Mac users:

To get the visualization of the hierarchy looking nice sometimes takes a little effort. To get graphs to compile correctly do the following. Using "brew" to install, you need to do "brew install gts" followed by "brew install --with-gts graphviz". The (hacky) way that the visualizations are produced is the following. The code, vis_corex.py, produces a text file called "graphs/graph.dot". This just encodes the edges between nodes in dot format. Then, the code calls a command line utility called sfdp that is part of graphviz,

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
These dot files can also be opened with OmniGraffle if you would like to be able to manipulate them by hand. If you want, you can try to recompile graphs yourself with different options to make them look nicer. Or you can edit the dot files to get effects like colored nodes, etc.

Also, note that you can color nodes in the graphs by putting prepending a color to column label names in the CSV file. For instance, blue_column_1_label_name will show column_1_label_name in blue in the graphs folder. Any matplotlib colors are allowed. See the BIG5 data file and graphs produced by the command line utility.

from corex.

paseman avatar paseman commented on May 26, 2024

from corex.

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