Edited VitePress site to include nav bar, different colors, and link …

…paper

homepage/.vitepress/config.mjs

@@ -3,7 +3,7 @@ import { defineConfig } from "vitepress";
 // https://vitepress.dev/reference/site-config
 export default defineConfig({
   lang: "en-US",
-  title: "Deep mutational scanning of Lassa virus Josiah strain glycoprotein complex (GPC)",
+  title: "Lassa GPC DMS",
   description:
     "Interactive figures and detailed results for deep mutational scanning of the GPC from the lineage IV Lassa virus Josiah strain.",
   base: "/LASV_Josiah_GP_DMS",
@@ -12,6 +12,9 @@ export default defineConfig({
     // https://vitepress.dev/reference/default-theme-config
     nav: [
       { text: "Home", link: "/" },
+      { text: 'Paper', link: "https://www.biorxiv.org/content/10.1101/2024.02.05.579020v1" },
+      { text: 'Cell Entry', link: '/cell_entry' },
+      { text: 'Antibody Escape', link: '/antibody_escape' },
       { text: "Appendix", link: "/appendix", target: "_self" },
     ],
     socialLinks: [{ icon: "github", link: "https://github.com/dms-vep/LASV_Josiah_GP_DMS.git" }],

homepage/.vitepress/theme/style.css

@@ -22,13 +22,13 @@
   --vp-home-hero-name-color: transparent;
   --vp-home-hero-name-background: -webkit-linear-gradient(
     200deg,
-    #40a5dd,
-    #ce6767
+    #0072B2,
+    #E69F00
   );
   --vp-home-hero-image-background-image: -webkit-linear-gradient(
     -45deg,
-    #40a5dd 50%,
-    #ce6767 50%
+    #0072B2 50%,
+    #E69F00 50%
   );
   --vp-home-hero-image-filter: blur(100px);
 }

homepage/antibody_escape.md

@@ -1,12 +1,10 @@
 ---
-aside: false
+aside: true
 ---
 
 # Escape from monoclonal antibodies
 
-## Interactive plots of mutation effects for monoclonal antibodies
-
-The plots below show how mutations affect neutralization by a panel of monoclonal antibodies (25.10C, 12.1F, 37.7H, 25.6A, 37.2D, and 8.9F). The plots are interactive, and allow you to zoom and mouseover sites and mutations.
+The plots below show how mutations affect neutralization by a panel of monoclonal antibodies (25.10C, 12.1F, 37.7H, 25.6A, 37.2D, and 8.9F). The plots are interactive, and allow you to zoom and mouseover sites and mutations. Positive values indicate reduced neutralization by antibody while negative values indicate more neutralization.
 
 Here is an explanation of the key elements for each plot:
  - The zoom bar at the top of the plot shows different regions of GPC, and can be used to zoom in on specific sites.
@@ -17,47 +15,48 @@ Here is an explanation of the key elements for each plot:
    function (and grays out mutations that are more deleterious). You can also select to floor the escape at zero to show / not show "negative" escape values. 
 
 
-### Antibody 25.10C
+## Antibody 25.10C
 - The plot below shows how mutations affect neutralization by the monoclonal antibody 25.10C. Click on the expansion box in the upper right of the plot to enlarge it for easier viewing, or [click here](/htmls/2510C_mut_effect.html){target="_self"} to open the plot in a stand-alone window.
 
 <Figure caption="Interactive plot showing effects of mutations on antibody 25.10C escape">
     <Altair :showShadow="true" :spec-url="'htmls/2510C_mut_effect.html'"></Altair>
 </Figure>
 
-### Antibody 12.1F
+## Antibody 12.1F
 - The plot below shows how mutations affect neutralization by the monoclonal antibody 12.1F. Click on the expansion box in the upper right of the plot to enlarge it for easier viewing, or [click here](/htmls/121F_mut_effect.html){target="_self"} to open the plot in a stand-alone window.
 
 <Figure caption="Interactive plot showing effects of mutations on antibody 12.1F escape">
     <Altair :showShadow="true" :spec-url="'htmls/121F_mut_effect.html'"></Altair>
 </Figure>
 
-### Antibody 37.7H
+## Antibody 37.7H
 - The plot below shows how mutations affect neutralization by the monoclonal antibody 37.7H. Click on the expansion box in the upper right of the plot to enlarge it for easier viewing, or [click here](/htmls/377H_mut_effect.html){target="_self"} to open the plot in a stand-alone window.
 
 <Figure caption="Interactive plot showing effects of mutations on antibody 37.7H escape">
     <Altair :showShadow="true" :spec-url="'htmls/377H_mut_effect.html'"></Altair>
 </Figure>
 
-### Antibody 25.6A
+## Antibody 25.6A
 - The plot below shows how mutations affect neutralization by the monoclonal antibody 25.6A. Click on the expansion box in the upper right of the plot to enlarge it for easier viewing, or [click here](/htmls/256A_mut_effect.html){target="_self"} to open the plot in a stand-alone window.
 
 <Figure caption="Interactive plot showing effects of mutations on antibody 25.6A escape">
     <Altair :showShadow="true" :spec-url="'htmls/256A_mut_effect.html'"></Altair>
 </Figure>
 
-### Antibody 37.2D
+## Antibody 37.2D
 - The plot below shows how mutations affect neutralization by the monoclonal antibody 37.2D. Click on the expansion box in the upper right of the plot to enlarge it for easier viewing, or [click here](/htmls/372D_mut_effect.html){target="_self"} to open the plot in a stand-alone window.
 
 <Figure caption="Interactive plot showing effects of mutations on antibody 37.2D escape">
     <Altair :showShadow="true" :spec-url="'htmls/372D_mut_effect.html'"></Altair>
 </Figure>
 
-### Antibody 8.9F
+## Antibody 8.9F
 - The plot below shows how mutations affect neutralization by the monoclonal antibody 8.9F. Click on the expansion box in the upper right of the plot to enlarge it for easier viewing, or [click here](/htmls/89F_mut_effect.html){target="_self"} to open the plot in a stand-alone window.
 
 <Figure caption="Interactive plot showing effects of mutations on antibody 8.9F escape">
     <Altair :showShadow="true" :spec-url="'htmls/89F_mut_effect.html'"></Altair>
 </Figure>
 
 ## Numerical values of escape
+
 For per-antibody escape values, see [these CSV files](https://github.com/dms-vep/LASV_Josiah_GP_DMS/tree/main/results/filtered_antibody_escape_CSVs).

homepage/cell_entry.md

@@ -5,19 +5,20 @@ aside: false
 # Effects of mutations on pseudovirus entry in 293T cells 
 
 ## Interactive plot of mutation effects
-The plot below shows how mutations affect cell entry, and allows you to zoom and mouseover sites and mutations. 
-Click on the expansion box in the upper right of the plot to enlarge it for easier viewing, or [click here](/htmls/293T_entry_func_effects.html){target="_self"} to open the plot in a stand-alone window.
-
-<Figure caption="Interactive plot showing effects of mutations on entry into 293T cells">
-    <Altair :showShadow="true" :spec-url="'htmls/293T_entry_func_effects.html'"></Altair>
-</Figure>
+The plot below shows how mutations affect cell entry, and allows you to zoom and mouseover sites and mutations. Positive values indicate better entry than the parental GPC while negative values indicate impaired entry. 
 
 Here is an explanation of the key plot elements:
  - The zoom bar at the top of the plot shows different regions of GPC, and can be used to zoom in on specific sites.
  - The line plot summarizes the effects of mutations at each site, using the site smmary statistic specified by the interactive option at the bottom of the plot (eg, sum or mean effect of mutations at a site).
   - The heatmap shows how each individual mutation affects cell entry. The `x`'s indicate the amino-acid identity in the parental GPC strain, light gray indicates mutations that were not measured, and dark gray indicates mutations that are filtered out by one of the interactive sliders at the bottom of the plot. If you mouseover points, you can also see the measurement in each individual library, which provides a sense of the reproducibility between experiments. 
   - The options at the bottom of the plot allow you to adjust what is displayed. For instance, the *times_seen* slider filters for only mutations seen in at least that many unique variants per-library; larger values will generally give more accurate measurements. Similarly, you can filter by how many different experimental selections the mutation was measured in. You can also select to only show mutations accessible by some number of mutations to the codon in the parental sequence (eg, only accessible by single-nucleotide mutations).
 
+Click on the expansion box in the upper right of the plot to enlarge it for easier viewing, or [click here](/htmls/293T_entry_func_effects.html){target="_self"} to open the plot in a stand-alone window.
+
+<Figure caption="Interactive plot showing effects of mutations on entry into 293T cells">
+    <Altair :showShadow="true" :spec-url="'htmls/293T_entry_func_effects.html'"></Altair>
+</Figure>
+
 ## Numerical values of mutation effects on cell entry
-The numerical data plotted on this page are available in [this CSV file](https://github.com/dms-vep/LASV_Josiah_GP_DMS/blob/main/results/func_effects/averages/293T_entry_func_effects.csv).
-Note that these values have **not** been filtered by QC criteria like the *times seen*, so either make sure you understand the filters in the file or use the pre-filtered numerical values provided [here](https://github.com/dms-vep/LASV_Josiah_GP_DMS/blob/main/results/filtered_func_effect_CSVs/293T_filtered_func_effects.csv).
+The pre-filtered numerical data plotted on this page can be found [here](https://github.com/dms-vep/LASV_Josiah_GP_DMS/blob/main/results/filtered_func_effect_CSVs/293T_filtered_func_effects.csv). Alternatively, unfiltered data are available in [this CSV file](https://github.com/dms-vep/LASV_Josiah_GP_DMS/blob/main/results/func_effects/averages/293T_entry_func_effects.csv).
+Note that these values have **not** been filtered by QC criteria like the *times seen*, so either make sure you understand the filters in the file or use the pre-filtered data.

homepage/index.md

@@ -12,7 +12,7 @@ features:
   - title: Cell entry
     details: Effects of mutations on pseudovirus entry in 293T cells
     link: /cell_entry
-  - title: antibody escape
+  - title: Antibody escape
     details: Effects of mutations on neutralization by monoclonal antibodies
     link: /antibody_escape
   - title: Interactive phylogenetic tree
@@ -27,7 +27,7 @@ features:
 ---
 
 ## About this site
-This website contains interactive plots and numerical results from [pseudovirus deep mutational scanning](https://doi.org/10.1016/j.cell.2023.02.001) experiments that measure the effects of mutations to the glycoprotein complex (GPC) of the lineage IV Lassa virus Josiah strain on cell entry and antibody escape.
+This website contains interactive plots and numerical results from a [study](https://www.biorxiv.org/content/10.1101/2024.02.05.579020v1) that measures the effects of mutations to the glycoprotein complex (GPC) of the lineage IV Lassa virus Josiah strain on cell entry and antibody escape using [pseudovirus deep mutational scanning](https://www.sciencedirect.com/science/article/pii/S0092867423001034?via%3Dihub).
 This study was led by Caleb Carr and Kate Crawford in the Bloom lab.
 
 The links in the boxes above take you to interactive plots or descriptions of different aspects of the study.

homepage/summary.md

@@ -5,15 +5,18 @@ aside: false
 # Summary of how mutations affect both antibody escape and cell entry
 
 ## Interactive plot of both antibody escape and cell entry
-The plot below shows how mutations affect antibody escape from all six antibodies and cell entry, and allows you to zoom and mouseover sites and mutations. 
-Click on the expansion box in the upper right of the plot to enlarge it for easier viewing, or [click here](/htmls/phenotypes_faceted.html){target="_self"} to open the plot in a stand-alone window.
-
-<Figure caption="Interactive plot showing effects of mutations on all phenotypes">
-    <Altair :showShadow="true" :spec-url="'htmls/phenotypes_faceted.html'"></Altair>
-</Figure>
+The plot below shows how mutations affect antibody escape from all six antibodies and cell entry, and allows you to zoom and mouseover sites and mutations. Positive cell entry values indicate better entry than the parental GPC while negative values indicate impaired entry. Positive escape values indicate reduced neutralization by an antibody while negative values indicate more neutralization.
 
 Here is an explanation of the key plot elements:
  - The zoom bar at the top of the plot shows different regions of GPC, and can be used to zoom in on specific sites.
  - The line plots summarize the average escape from neutralization by all six monoclonal antibodies, and then below that in gray the escape for each individual antibody. The height of each line summarizes the total escape caused by mutations at each site using the *site escape statistic* specified by the interactive options at the bottom of the plot.
   - The heatmaps show how each individual mutation affects each phenotype. The `x`'s indicate the amino-acid identity in the parental GPC strain, light gray indicates mutations that were not measured, and dark gray indicates mutations that are filtered out by one of the interactive sliders at the bottom of the plot (eg, they have a very negative effect on cell entry). You can mouse over any of the points for details.
   - The options at the bottom of the plot allow you to interactively adjust what is displayed. For instance, the *minimum mutation entry in 293T cells* only shows mutations with at least some minimal cell entry function (and grays out mutations that are more deleterious). You can also select to floor the escape at zero to show / not show "negative" escape values.
+
+Click on the expansion box in the upper right of the plot to enlarge it for easier viewing, or [click here](/htmls/phenotypes_faceted.html){target="_self"} to open the plot in a stand-alone window.
+
+<Figure caption="Interactive plot showing effects of mutations on all phenotypes">
+    <Altair :showShadow="true" :spec-url="'htmls/phenotypes_faceted.html'"></Altair>
+</Figure>
+
+