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scTDA works well without an Ayasdi account, as indicated in the tutorial. To that end use the topological representation generated through TopologicalRepresentation.save(). For instance, in section 3 of the tutorial you could use the following command to load the representation produced in section 2 through TopologicalRepresentation.save():
c = scTDA.RootedGraph('Embryo_pca_25_0.40', 'Embryo.no_subsampling.tsv', groups=False)
Please make sure that you have installed the most recent update of scTDA. To that end, uninstall the installed version, clone this repository using git, and install the most recent version using:
sudo python setup.py install
For optimal visualization, it is also strongly recommended to have graphviz installed.
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