Add the vertical navigation.

aspar.scss

@@ -18,6 +18,10 @@ $custom-secondary-transform: bold !default;
 // colors
 $body-bg: #05347E;
 $body-color: white !default;
+a {
+  color: hotpink;
+}
+
 $link-color: #FFC900 !default;
 $selection-bg: rgba(78, 92, 104, 0.99) !default;
 
@@ -28,6 +32,14 @@ $presentation-h1-fontcolor: #FEDA5E !default;
 // code blocks
 $code-block-bg: transparent !default;
 
+.alert {
+  color: lighten(#FFC900, 25%);
+  font-weight: bold;
+}
+
+section.level1 {
+    top: 0px !important;
+}
 
 /*-- scss:rules --*/
 
@@ -36,6 +48,7 @@ $code-block-bg: transparent !default;
   font-family: $custom-main-family;
   text-transform: $custom-main-transform;
   font: $custom-font;
+  link-color: $link-color;
 }
 
 .reveal section h2 {
@@ -43,6 +56,7 @@ $code-block-bg: transparent !default;
   font-family: $custom-family;
   text-transform: $custom-secondary-transform;
   font: $custom-font;
+  link-color: $link-color;
 }
 
 .reveal section h3 {
@@ -50,6 +64,7 @@ $code-block-bg: transparent !default;
   font-family: $custom-family;
   text-transform: $custom-secondary-transform;
   font: $custom-font;
+  link-color: $link-color;
 }
 
 .reveal section h4 {
@@ -61,4 +76,5 @@ $code-block-bg: transparent !default;
 
 .reveal .slide title {
     link-color: yellow;
-}
\ No newline at end of file
+}
+

presentation.qmd

@@ -2,14 +2,17 @@
 title: "FAIR data for a better understanding of fungal epidemiology"
 author:
   - name: "[Sibbe Bakker](https://orcid.org/0009-0001-0696-1684)"
-    affiliation: Bioinformatics
+    affiliation: Genetics
   - name: "Anna Fensel"
     affiliation: AI & Data science
 format: 
     revealjs:
-        self-contained: true
-        csl:  diabetologia.csl
+        csl: diabetologia.csl
         theme: aspar.scss
+        standalone: true
+        embed-resources: true
+        navigation-mode: vertical
+        controls-layout: bottom-right
 title-slide-attributes:
     data-background-size: cover
     data-background-image: inclusions/blurred-asper.jpg
@@ -18,46 +21,63 @@ date: "2024-01-15"
 bibliography: "BibDataBase.bib"
 ---
 
-## Relivance of fungal pathogens
+# Relivance of fungi {background-color="black" background-image="inclusions/blurred-asper.jpg" background-size="cover" background-opacity="0.5"}
 
 ![The priority fungal pathogens identified by
 the WHO [@worldhealthorganizationwhoWHOFungalPriority2022]](
 inclusions/who-priorities.png)
 
-## A closer look at _A. fumigatus_
+::: notes
+
+Highlight what these fungi are, how important are they and where?
+
+:::
+
+---
+
+## A closer look at _A. fumigatus_ {background-color="black" background-image="inclusions/blurred-asper.jpg" background-size="cover" background-opacity="0.5"}
 
 <!-- Why are we looking here? Because the genetics department does a lot of
 work with it -->
 
-* Why? Because the WUR has expertise on _A. fumigatus_.
-* It is important for Dutch public health. <br> _Due to the large tulip sector here._
+::: columns
 
-## The knowledge gap
+::: {.column width="60%"}
 
-::: {.r-stack}
+* Why? Because the WUR has [expertise]{.alert} on _A. fumigatus_.
+* It is [imporant]{.alert} for Dutch public health. <br> _Due to the large tulip sector here._
 
-::: {.fragment fragment-index=1 .fade-out}
+:::
 
-> Being able to track the evolution of fungal pathogens.
+::: {.column width="40%"}
+
+![Conidia of _A. fumigatus_ [@OneHealthFungal2019]](inclusions/aspergillus-fromNBK54998.jpg)
 
 :::
 
-::: {.fragment fragment-index=2 .fade-in-then-out}
+:::
 
-* This is called phylogeography.
 
-:::
+# The knowledge gap {background-color="black" background-image="inclusions/blurred-asper.jpg" background-size="cover" background-opacity="0.5"}
+
+## What we need to do {background-color="black" background-image="inclusions/blurred-asper.jpg" background-size="cover" background-opacity="0.5"}
+
+> Being able to track the evolution of fungal pathogens.
+
+## How do we do it? {background-color="black" background-image="inclusions/blurred-asper.jpg" background-size="cover" background-opacity="0.5"}
+
+phylogeography.
+
+## Nextstrain {background-color="black" background-image="inclusions/blurred-asper.jpg" background-size="cover" background-opacity="0.5"}
 
-::: {.fragment fragment-index=3 .fade-in-then-out}
 Using `nextstrain` for fungal pathogens [@hadfieldNextstrainRealtimeTracking2018]. An example:
 
 ![Overview of the spread of west-nile in the USA from 
 [nextstrain](https://nextstrain.org/narratives/twenty-years-of-WNV?n=3).
 ](inclusions/west-nile.png)
-:::
 
 
-::: {.fragment fragment-index=4 .fade-in-then-out}
+## Bridging the gap {background-color="black" background-image="inclusions/blurred-asper.jpg" background-size="cover" background-opacity="0.5"}
 
 > This has not yet been done because $\dots$
 
@@ -65,11 +85,8 @@ Using `nextstrain` for fungal pathogens [@hadfieldNextstrainRealtimeTracking2018
 
 * Standardisation is not a focus in the _A. fumigatus_ domain.
 
-:::
-
-:::
 
-## Method
+# Method {background-color="black" background-image="inclusions/blurred-asper.jpg" background-size="cover" background-opacity="0.5"}
 
 1. Harmonise _existent_ metadata.
 
@@ -79,7 +96,7 @@ Using `nextstrain` for fungal pathogens [@hadfieldNextstrainRealtimeTracking2018
 
 4. Generalise the workflow to other fungi.
 
-## Outlook
+# Outlook {background-color="black" background-image="inclusions/blurred-asper.jpg" background-size="cover" background-opacity="0.5"}
 
 * This would represent an innovation in the fungal database field.
 
@@ -88,4 +105,4 @@ on the _ITS_ sequence.
 
 * The solution could be generalised to plant epidemiology also.
 
-## References
\ No newline at end of file
+# References {background-color="black" background-image="inclusions/blurred-asper.jpg" background-size="cover" background-opacity="0.5"}
\ No newline at end of file

todo

+Make the link colour yellow again.