Jan suggestions (fig labels)
authorFabio Zanini <fabio.zanini@tuebingen.mpg.de>
Tue, 26 Feb 2013 16:26:51 +0000 (17:26 +0100)
committerFabio Zanini <fabio.zanini@tuebingen.mpg.de>
Tue, 26 Feb 2013 16:26:51 +0000 (17:26 +0100)
figures/Shankarappa_allele_freqs_trajectories_nonsyn_p10.pdf
figures/Shankarappa_allele_freqs_trajectories_nonsyn_p10.svg
figures/Shankarappa_allele_freqs_trajectories_syn_p10.pdf
figures/Shankarappa_allele_freqs_trajectories_syn_p10.svg
figures/fixation_probabilities_VnonV.pdf
figures/fixation_probabilities_VnonV.svg
figures/reactivities_histograms_syn.pdf
figures/reactivities_histograms_syn.svg
synmut.tex

index a29e6e5..bd2d0a8 100644 (file)
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index 6e09c36..2662a0b 100644 (file)
@@ -1,7 +1,7 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % ARTICLE ABOUT FATE OF SYNONYMOUS MUTATIONS IN HIV
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\documentclass[rmp, onecolumn]{revtex4}
+\documentclass[rmp, twocolumn]{revtex4}
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \usepackage[english]{babel}
@@ -224,9 +224,9 @@ have been experiencing selection for some time already, tend to be neutral.
 
 \begin{figure}
 \begin{center}
-\subfloat{\includegraphics[width=0.9\linewidth]{fixation_times}
+\subfloat{\includegraphics[width=0.9\linewidth]{fixation_times.pdf}
 \label{fig:fixp1}}\\
-\subfloat{\includegraphics[width=0.9\linewidth]{fixation_probabilities}
+\subfloat{\includegraphics[width=0.9\linewidth]{fixation_probabilities.pdf}
 \label{fig:fixp2}}
 \caption{Fixation and loss of synonymous mutations.
 Panel A) shows the fraction of polymorphisms that have fixed (lower curves),
@@ -292,9 +292,8 @@ its human host cells at the macroevolutionary level \citep{kuyl_biased_2012}.
 
 \begin{figure}
 \begin{center}
-\subfloat{\includegraphics[height=0.46\linewidth]{reactivities_histograms_syn}
-\label{fig:SHAPEA}}
-\subfloat{\includegraphics[height=0.46\linewidth]{fixation_probabilities_VnonV}\label{fig:SHAPEB}}
+\subfloat{\includegraphics[height=0.47\linewidth]{reactivities_histograms_syn.pdf}\label{fig:SHAPEA}}
+\subfloat{\includegraphics[height=0.46\linewidth]{fixation_probabilities_VnonV.pdf}\label{fig:SHAPEB}}
 \caption{Permissible synonymous mutations tend to be unpaired.
 Panel A) shows the distribution of SHAPE reactivities among synonymous mutations
 that fix, mutations that reach frequencies above 15\%, but
@@ -561,7 +560,7 @@ studies \citep{shankarappa_consistent_1999, liu_selection_2006,
 bunnik_autologous_2008} and downloaded from the Los Alamos National Laboratory
 (LANL) HIV sequence database~\citep{LANL2012}. The samples from some patients
 show substantial population structure and were discarded (see
-\figurename~S\PCApa); a total of 11 patients with 4-23 time points each and
+\figurename~S\PCApat); a total of 11 patients with 4-23 time points each and
 approximately 10 sequences per time point were analyzed. The time intervals
 between two consecutive sequences ranged from 1 to 34 months, most of them
 between 6 and 10 months.