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Rename figures for elife

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sidneymbell committed May 2, 2019
1 parent 35a20d1 commit 3cf083982790bd590250354fe2bf7dc36faec36a
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@@ -146,7 +146,7 @@ \section*{Introduction}

\begin{figure}[ht]
\begin{centering}
\includegraphics[width=\linewidth]{../figures/png/titer_tree_heatmap.png}
\includegraphics[width=\linewidth]{../figures/png/figure1.png}
\caption{\textbf{Phylogeny of dengue virus sequences and normalized antigenic distances.}
\textbf{(A)} Maximum likelihood phylogeny of the \textit{E} (envelope) gene from titered dengue viruses.
Notably, each of the four serotypes contains substantial genetic diversity.
@@ -215,7 +215,7 @@ \subsection*{Dengue antigenic evolution corresponds to genetic divergence}

\begin{figure}[ht]
\begin{centering}
\includegraphics[width=\textwidth]{../figures/png/mutations_position_db.png}
\includegraphics[width=\textwidth]{../figures/png/figure2.png}
\caption{\textbf{Distribution and effect size of antigenic mutations.}
Each point represents one antigenically relevant mutation or colinear mutation cluster.
Clustered mutations are connected with dashed lines with point size proportionate to cluster size (N=2--6).
@@ -234,7 +234,7 @@ \subsection*{Dengue antigenic evolution corresponds to genetic divergence}
\subsection*{Each serotype of dengue contains moderate antigenic heterogeneity}
\begin{figure}[ht]
\begin{centering}
\includegraphics[width=\textwidth]{../figures/png/vaccine_titer_trees.png}
\includegraphics[width=\textwidth]{../figures/png/figure3.png}
\caption{\textbf{Antigenic distance from NIH vaccine strains.} By assigning a discrete increment of antigenic change to each mutation, we can estimate the asymmetrical antigenic distance between any serum strain and test virus strain based on their genetic differences. Here, we show the estimated antigenic distance between serum raised against each monovalent component of the NIH vaccine candidate (indicated as `X') and each test virus in the tree.}
\label{vaccine_titer_trees}
\end{centering}
@@ -247,7 +247,7 @@ \subsection*{Each serotype of dengue contains moderate antigenic heterogeneity}

\begin{figure}[ht]
\centering
\includegraphics[width=0.75\textwidth]{../figures/png/genotype_dTiter_heatmap.png}
\includegraphics[width=0.75\textwidth]{../figures/png/figure4.png}
\caption{\textbf{Titer distance by genotype.}
Values represent the mean interpolated antigenic distance between canonical dengue genotypes (in standardized log$_2$ titer units).
}
@@ -279,7 +279,7 @@ \subsection*{Antigenic novelty predicts serotype success}

\begin{figure}[ht]
\begin{centering}
\includegraphics[width=\linewidth]{../figures/png/serotype_fitness_model.png}
\includegraphics[width=\linewidth]{../figures/png/figure5.png}
\caption{\textbf{Antigenic novelty predicts serotype success.}
\textbf{(A)} The relative frequency of each serotype, $x_i$, in Southeast Asia estimated every three months based on available sequence data.
\textbf{(B)} Total fitness of each serotype. We calculate antigenic fitness for each serotype over time as its frequency-weighted antigenic distance from recently circulating viruses.
@@ -331,7 +331,7 @@ \subsection*{Antigenic novelty also partially predicts genotype success}

\begin{figure}[ht]
\begin{centering}
\includegraphics[width=\linewidth]{../figures/png/genotype-fitness.png}
\includegraphics[width=\linewidth]{../figures/png/figure6.png}
\caption{\textbf{Antigenic novelty partially predicts genotype success }
\textbf{(A)} Relative frequencies of each canonical dengue genotype across Southeast Asia, estimated from available sequence data.
\textbf{(B)} Antigenic fitness is calculated for each genotype as its frequency-weighted antigenic distance from recently circulating genotypes.
@@ -804,7 +804,7 @@ \section*{Supplement}

\begin{figure}[ht]
\centering
\includegraphics[width=0.75\textwidth]{../figures/png/titer_asymmetry.png}
\includegraphics[width=0.75\textwidth]{../figures/png/figure1-supplement1.png}
\caption{\textbf{Titer value symmetry.}
Some viruses have greater avidity overall, and some sera are more potent overall.
We normalize for these row and column effects ($v_a$ and $p_b$, respectively) in the titer model.
@@ -815,7 +815,7 @@ \section*{Supplement}

\begin{figure}[ht]
\centering
\includegraphics[width=0.75\textwidth]{../figures/png/titer_species_error.png}
\includegraphics[width=0.75\textwidth]{../figures/png/figure2-supplement1.png}
\caption{\textbf{Titer prediction error by serum strain and species.}
Human sera was raised against four different virus strains (the monovalent vaccine components); non-human primate (NHP) sera was raised against many different virus strains.
Here, we excluded NHP sera raised against the monovalent vaccine components, such that each normalized titer measurement is aggregated across individuals, but not across species.
@@ -826,7 +826,7 @@ \section*{Supplement}

\begin{figure}[ht]
\centering
\includegraphics[width=\textwidth]{../figures/png/thai_frequencies_comparison.png}
\includegraphics[width=\textwidth]{../figures/png/figure5-supplement1.png}
\caption{\textbf{Case counts versus clade frequencies in Thailand.}
As described in the Methods, we estimate clade frequencies based on observed relative abundance in the `slice' of the phylogeny at each quarterly timepoint.
These frequency estimates are smoothed using a discretized Brownian motion diffusion process.
@@ -838,7 +838,7 @@ \section*{Supplement}

\begin{figure}[ht]
\centering
\includegraphics[width=\textwidth]{../figures/png/phylogeny_homoplasy.png}
\includegraphics[width=\textwidth]{../figures/png/figure2-supplement2.png}
\caption{\textbf{Genotype as site E 390 across dengue phylogeny.}
Dengue virus genotypes can be seen on Nextstrain \citep{hadfield2018nextstrain}.
A live view of this figure is available at \href{https://nextstrain.org/dengue/}{nextstrain.org/dengue/}.}
@@ -847,7 +847,7 @@ \section*{Supplement}

\begin{figure}[ht]
\centering
\includegraphics[width=\textwidth]{../figures/png/simulated_frequencies_high_beta.png}
\includegraphics[width=\textwidth]{../figures/png/figure5-supplement2.png}
\caption{\textbf{Simulated serotype frequencies.}
As described in the Methods, we seeded a simulation with two years of empirical frequencies and predicted forward to simulate the remainder of the timecourse.
Here, we simulated under the model parameters described in Table~\ref{simulation_parameters}}
@@ -856,7 +856,7 @@ \section*{Supplement}

\begin{figure}[ht]
\centering
\includegraphics[width=\textwidth]{../figures/png/simulated_fitParameters_freqs.png}
\includegraphics[width=\textwidth]{../figures/png/figure5-supplement3.png}
\caption{\textbf{Simulated serotype frequencies (model parameters).}
As described in the Methods, we seeded a simulation with two years of empirical frequencies and predicted forward to simulate the remainder of the timecourse.
Here, we simulated under the model parameters described in Table~\ref{fitness_model_parameters}.

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