Update defaults to match those used in the corresponding publication #35
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Changes the default encoding of alignment inputs for PCA embedding and t-SNE initialization by PCA from "integer" to "simplex".
Changes min samples per cluster from 5 to 10 to match the defaults we used in the corresponding publication.
huddlej
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Changes the defaults for pathogen-embed and pathogen-cluster to match the defaults we used in the corresponding "cartography" paper including: