diff --git a/tests/pathogen-embed-t-sne-pca-encoding-by-simplex.t b/tests/pathogen-embed-t-sne-pca-encoding-by-simplex.t
new file mode 100644
index 0000000..f973215
--- /dev/null
+++ b/tests/pathogen-embed-t-sne-pca-encoding-by-simplex.t
@@ -0,0 +1,14 @@
+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) ]]