Merge pull request #131 from blab/increase-figure-resolution

Prepare editable version of final paper

cartography.yml

@@ -11,8 +11,8 @@ dependencies:
   - treetime=0.10.1
   - pip=21.1.3
   - seaborn=0.11.1
-  - altair=5.0.1
-  - vl-convert-python=0.11.1
+  - altair=5.4.1
+  - vl-convert-python=1.6.1
   - python=3.*
   - scikit-learn=0.24.2
   - umap-learn=0.5.*

ha-na-nextstrain/2022-02-23-seasonal-flu-ha-na-reassortment.ipynb

@@ -575,7 +575,7 @@
    "outputs": [],
    "source": [
     "pca_final_chart.save(output_pca_html)\n",
-    "pca_final_chart.save(output_pca_png, format=\"png\", scale_factor=2.0)"
+    "pca_final_chart.save(output_pca_png, format=\"png\", ppi=300)"
    ]
   },
   {
@@ -768,7 +768,7 @@
    "outputs": [],
    "source": [
     "mds_final_chart.save(output_mds_html)\n",
-    "mds_final_chart.save(output_mds_png, format=\"png\", scale_factor=2.0)"
+    "mds_final_chart.save(output_mds_png, format=\"png\", ppi=300)"
    ]
   },
   {
@@ -946,7 +946,7 @@
    "outputs": [],
    "source": [
     "tsne_final_chart.save(output_tsne_html)\n",
-    "tsne_final_chart.save(output_tsne_png, format=\"png\", scale_factor=2.0)"
+    "tsne_final_chart.save(output_tsne_png, format=\"png\", ppi=300)"
    ]
   },
   {
@@ -1028,7 +1028,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "tsne_mcc_counts_chart.save(output_tsne_mcc_counts_png, format=\"png\", scale_factor=2.0)"
+    "tsne_mcc_counts_chart.save(output_tsne_mcc_counts_png, format=\"png\", ppi=300)"
    ]
   },
   {
@@ -1276,7 +1276,7 @@
    "outputs": [],
    "source": [
     "umap_final_chart.save(output_umap_html)\n",
-    "umap_final_chart.save(output_umap_png, format=\"png\", scale_factor=2.0)"
+    "umap_final_chart.save(output_umap_png, format=\"png\", ppi=300)"
    ]
   },
   {
@@ -1576,7 +1576,7 @@
    "outputs": [],
    "source": [
     "chart_embeddings.save(output_full_html)\n",
-    "chart_embeddings.save(output_full_png, format=\"png\", scale_factor=2.0)"
+    "chart_embeddings.save(output_full_png, format=\"png\", ppi=300)"
    ]
   },
   {
@@ -1617,7 +1617,7 @@
    "outputs": [],
    "source": [
     "ha_na_only_chart.save(output_ha_na_html)\n",
-    "ha_na_only_chart.save(output_ha_na_png, format=\"png\", scale_factor=2.0)"
+    "ha_na_only_chart.save(output_ha_na_png, format=\"png\", ppi=300)"
    ]
   },
   {

manuscript/build.sh

@@ -13,3 +13,7 @@ pdflatex -draftmode ${TITLE}
 bibtex ${TITLE}
 pdflatex -draftmode ${TITLE}
 pdflatex ${TITLE}
+
+pdflatex -draftmode ${TITLE}_supplement
+pdflatex -draftmode ${TITLE}_supplement
+pdflatex ${TITLE}_supplement

manuscript/cartography.tex

@@ -788,6 +788,4 @@ \subsection*{Funding}
 \bibliographystyle{unsrt}
 \bibliography{cartography}
 
-\include{cartography_supplement}
-
 \end{document}

manuscript/cartography_supplement.tex

@@ -1,3 +1,32 @@
+\documentclass[webpdf,contemporary,large,single]{oup-authoring-template}
+\onecolumn % for one column layouts
+
+%\usepackage{showframe}
+
+\graphicspath{{Fig/}}
+
+% line numbers
+%\usepackage[mathlines, switch]{lineno}
+\usepackage[right]{lineno}
+
+\theoremstyle{thmstyleone}%
+\newtheorem{theorem}{Theorem}%  meant for continuous numbers
+%%\newtheorem{theorem}{Theorem}[section]% meant for sectionwise numbers
+%% optional argument [theorem] produces theorem numbering sequence instead of independent numbers for Proposition
+\newtheorem{proposition}[theorem]{Proposition}%
+%%\newtheorem{proposition}{Proposition}% to get separate numbers for theorem and proposition etc.
+\theoremstyle{thmstyletwo}%
+\newtheorem{example}{Example}%
+\newtheorem{remark}{Remark}%
+\theoremstyle{thmstylethree}%
+\newtheorem{definition}{Definition}
+
+\usepackage{setspace}
+
+\begin{document}
+
+\nolinenumbers
+
 \section*{Supplementary data}
 
 \setcounter{figure}{0}
@@ -150,7 +179,7 @@ \section*{Supplementary data}
   Sequences from MCCs with fewer than 10 sequences are colored as ``unassigned''.
   Normalized VI values quantify the degree to which the combination of HA and NA sequences in an embedding reduces the distance of embedding clusters to TreeKnit reassortment groups represented by MCCs.
   MCC labels for larger pairs of reassortment events appear in each embedding at the average position on the x and y axis for sequences in a given MCC.
-  MCCs 14 and 11 represent a previously published reassortment event within Nextstrain clade A2 \citep{Potter2019}.
+  MCCs 14 and 11 represent a previously published reassortment event within Nextstrain clade A2.
   Labels for MCC 14 represents the sequences from clade A2.}\label{S_Fig_full_ha_na_embeddings}
 \end{figure}
 
@@ -276,3 +305,5 @@ \section*{Supplementary data}
 \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}
+
+\end{document}