Add missing S prefixes to fig references

manuscript/cartography.tex

@@ -320,7 +320,7 @@ \subsection{Joint embeddings of hemagglutinin and neuraminidase genomes identify
 Evolution of HA and NA surface proteins contributes to the ability of influenza viruses to escape existing immunity \citep{Petrova2018} and HA and NA genes frequently reassort \citep{Nelson2008,Marshall2013,Potter2019}.
 Therefore, we focused our reassortment analysis on HA and NA sequences, sampling 1,607 viruses collected between January 2016 and January 2018 with sequences for both genes.
 We inferred HA and NA phylogenies from these sequences and applied TreeKnit to both trees to identify maximally compatible clades (MCCs) that represent reassortment events \citep{Barrat-Charlaix2022}.
-Of the 208 reassortment events identified by TreeKnit, 15 (7\%) contained at least 10 samples representing 1,049 samples (65\%, Supplementary Fig.~\ref{S_Fig_ha_na_tangletree}).
+Of the 208 reassortment events identified by TreeKnit, 15 (7\%) contained at least 10 samples representing 1,049 samples (65\%, Supplementary Fig.~S\ref{S_Fig_ha_na_tangletree}).
 
 We created PCA, MDS, t-SNE, and UMAP embeddings from the HA alignments and from merged HA and NA alignments.
 We identified clusters in both HA-only and HA/NA embeddings and calculated the VI distance between these clusters and the MCCs identified by TreeKnit.
@@ -448,11 +448,11 @@ \subsection{SARS-CoV-2 clusters recapitulate broad genetic groups corresponding
 
 To understand whether t-SNE clusters could capture Pango-resolution genetic groups within a single Nextstrain clade, we evenly sampled approximately 2,000 sequences from a dominant Nextstrain clade with many Pango lineages, 21J (Delta), and identified clusters from a t-SNE embedding of those data.
 Within the 1,992 sequences sampled from 21J (Delta), we found 38 Pango lineages after collapsing lineages with fewer than 10 sequences into their parent lineages.
-We found 28 t-SNE clusters representing 1,806 sequences (91\%) with 186 sequences (9\%) assigned to the unclustered ``-1'' label (Supplementary Fig.~\ref{S_Fig_sarscov2_single_clade_embeddings_tsne_counts}).
+We found 28 t-SNE clusters representing 1,806 sequences (91\%) with 186 sequences (9\%) assigned to the unclustered ``-1'' label (Supplementary Fig.~S\ref{S_Fig_sarscov2_single_clade_embeddings_tsne_counts}).
 The VI distance between Pango lineages and all clusters (including the unclustered group) was 0.17 (Supplementary Table~\ref{S_Table_optimal_cluster_parameters}).
 This distance was consistent with the distance of 0.14 between Pango lineages and t-SNE clusters from both the full early and late SARS-CoV-2 datasets.
 The VI distance between Pango lineages and clusters without the unclustered sequences was 0.13, confirming that one quarter of the distance between t-SNE clusters and Pango lineages above came from unclustered sequences.
-Of the 38 Pango lineages with a t-SNE cluster, 30 lineages (79\%) had a single corresponding t-SNE cluster, seven lineages (18\%) had two or three t-SNE clusters, and one lineage (B.1.617.2) had five t-SNE clusters (Supplementary Fig.~\ref{S_Fig_sarscov2_single_clade_embeddings_tsne_counts}).
+Of the 38 Pango lineages with a t-SNE cluster, 30 lineages (79\%) had a single corresponding t-SNE cluster, seven lineages (18\%) had two or three t-SNE clusters, and one lineage (B.1.617.2) had five t-SNE clusters (Supplementary Fig.~S\ref{S_Fig_sarscov2_single_clade_embeddings_tsne_counts}).
 Of the 28 t-SNE clusters, 21 clusters (75\%) had a single corresponding Pango lineage, six (21\%) mapped to two or three Pango lineages, and one (cluster 27) mapped to 18 Pango lineages with most sequences from B.1.617.2 and AY.4.
 These results suggest that clusters from t-SNE embeddings can capture more Pango-resolution genetic groups by analyzing sequences within a specific Nextstrain clade.