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Add test for t-SNE with alternate PCA encoding
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huddlej committed Jul 2, 2024
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Run pathogen-embed with t-SNE on a H3N2 HA alignment.
Use the simplex encoding of the alignment for the PCA initialization.

$ pathogen-embed \
> --alignment $TESTDIR/data/h3n2_ha_alignment.fasta \
> --output-dataframe embed_t-sne.csv \
> t-sne \
> --perplexity 25 \
> --learning-rate 100 \
> --pca-encoding simplex

There should be one record in the embedding per input sequence in the alignment.

$ [[ $(sed 1d embed_t-sne.csv | wc -l) == $(grep "^>" $TESTDIR/data/h3n2_ha_alignment.fasta | wc -l) ]]

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