python hic_embeddings.py --infile connections.npy --outfile labelled_network_graph.html --name sample_name --k 2 --dimensions 2 --p 0.1 --q 0.5 --save_embeddings T
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--infile: A symmetric numpy matrix with dimensions$n \times n$ , where n is the number of scaffolds in the assembly, and each non-zero entry$a_{ij}$ and$a_{ji}$ indicates the presence of a connection between scaffolds i and j. Non-zero entries may be either actual counts or 1, but will be ignored by the script by default. The script hic_links.py in this repository may be used to generate a suitable matrix from a pair file generated by a scaffolding pipeline. -
--outfile: Path to a html file to save the labelled network graph to -
--save_embeddings: Whether to save a .npy array containing the embedding vectors (default = F, set to T to enable). -
--name: Sample name, used to name various output files generated by the script. -
Parameters
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--k: The number of clusters to use to label the embeddings (default = 2) -
--dimensions: The number of dimensions for the embedding vector. -
--p:$p$ parameter for node2vec (default = 1) -
--q:$q$ parameter for node2vec (default = 1)