Add example embeddings for recombinant lineages

Adds a supplementary figure showing two example MDS embeddings for late
SC2 samples from recombinant lineages and the corresponding parental
lineages.

Closes #91

manuscript/cartography.tex

@@ -426,7 +426,7 @@ \subsection{Distance-based embeddings reflect SARS-CoV-2 recombination events}
 We identified recombinant lineages that mapped closer to both of their parental lineages and those that mapped closer to at least one of the parental lineages.
 
 We identified 66 recombinant lineages for which that lineage and both of its parental lineages had at least 10 genomes (Supplementary Table~S\ref{S_Table_recombinant_distances}).
-MDS embeddings most consistently placed recombinant lineages between the parental lineages with correct placement of 60 lineages (91\%).
+MDS embeddings most consistently placed recombinant lineages between the parental lineages with correct placement of 60 (91\%) lineages (e.g., Supplementary Fig.~S\ref{S_Fig_sarscov2_late_embeddings_mds_recombinant_examples}).
 The t-SNE, UMAP, and PCA embeddings correctly placed 54 (82\%), 52 (79\%), and 40 (61\%) lineages, respectively.
 Additionally, all 66 recombinant lineages placed closer to at least one parent in all embeddings except for two lineages in the PCA embeddings.
 

manuscript/cartography_supplement.tex

@@ -171,3 +171,10 @@ \section*{Supplementary data}
 \includegraphics[width=\columnwidth]{figures/sarscov2-test-tsne-recombinant-counts-Nextstrain_clade.png}
 \caption{{\bf Number of late SARS-CoV-2 strains per combination of recombinant Pango lineage and t-SNE cluster where the count was at least 10 strains.}}\label{S_Fig_sarscov2_late_embeddings_tsne_recombinant_counts}
 \end{figure}
+
+\begin{figure}[!h]
+\includegraphics[width=0.75\columnwidth]{figures/sarscov2-test-mds-reassortment-XE-BA1-BA2.png}\\
+\includegraphics[width=0.75\columnwidth]{figures/sarscov2-test-mds-reassortment-XAS-BA2-BA5.png}
+\caption{{\bf Representative MDS embeddings (first two dimensions) of late SARS-CoV-2 samples filtered to known recombinant lineages and their parental lineages including A) XE which descended from BA.1 and BA.2 and B) XAS which descended from BA.2 and BA.5.}
+Larger circles represent the recombinant lineages in each figure.}\label{S_Fig_sarscov2_late_embeddings_mds_recombinant_examples}
+\end{figure}