deploy: 14766be

_sources/chapters/03_taxonomic_classification/intro.md

@@ -13,7 +13,13 @@ kernelspec:
 ---
 (taxonomic-classification)=
 # Taxonomic classification
-![Taxonomic classification workflow](../../images/workflows-taxonomic.png)
+```{figure} ../../images/workflows-taxonomic.png
+---
+name: workflows-taxonomy-fig
+width: 100%
+---
+Taxonomic classification workflow
+```
 
 ## Read-based classification overview
 Read-based classification is commonly used to determine the taxonomic groups present within a given sample. This technique 

_sources/chapters/04_functional_annotation/intro.md

@@ -13,7 +13,13 @@ kernelspec:
 ---
 (functional-annotation)=
 # Functional annotation
-![Functional annotation workflow](../../images/workflows-functional.png)
+```{figure} ../../images/workflows-functional.png
+---
+name: workflows-function-fig
+width: 100%
+---
+Functional annotation workflow
+```
 
 Functional annotation of **metagenome-assembled genomes (MAGs)** involves the identification and classification of genes 
 within these reconstructed genomes to understand their roles and potential functions. MAGs are recovered from DNA directly 

chapters/03_taxonomic_classification/intro.html

@@ -340,7 +340,12 @@ <h2> Contents </h2>
 
   <section class="tex2jax_ignore mathjax_ignore" id="taxonomic-classification">
 <span id="id1"></span><h1>Taxonomic classification<a class="headerlink" href="#taxonomic-classification" title="Link to this heading">#</a></h1>
-<p><img alt="Taxonomic classification workflow" src="../../_images/workflows-taxonomic.png" /></p>
+<figure class="align-default" id="workflows-taxonomy-fig">
+<a class="reference internal image-reference" href="../../_images/workflows-taxonomic.png"><img alt="../../_images/workflows-taxonomic.png" src="../../_images/workflows-taxonomic.png" style="width: 100%;" /></a>
+<figcaption>
+<p><span class="caption-number">Fig. 2 </span><span class="caption-text">Taxonomic classification workflow</span><a class="headerlink" href="#workflows-taxonomy-fig" title="Link to this image">#</a></p>
+</figcaption>
+</figure>
 <section id="read-based-classification-overview">
 <h2>Read-based classification overview<a class="headerlink" href="#read-based-classification-overview" title="Link to this heading">#</a></h2>
 <p>Read-based classification is commonly used to determine the taxonomic groups present within a given sample. This technique

chapters/04_functional_annotation/intro.html

@@ -328,7 +328,12 @@ <h1>Functional annotation</h1>
 
   <section class="tex2jax_ignore mathjax_ignore" id="functional-annotation">
 <span id="id1"></span><h1>Functional annotation<a class="headerlink" href="#functional-annotation" title="Link to this heading">#</a></h1>
-<p><img alt="Functional annotation workflow" src="../../_images/workflows-functional.png" /></p>
+<figure class="align-default" id="workflows-function-fig">
+<a class="reference internal image-reference" href="../../_images/workflows-functional.png"><img alt="../../_images/workflows-functional.png" src="../../_images/workflows-functional.png" style="width: 100%;" /></a>
+<figcaption>
+<p><span class="caption-number">Fig. 3 </span><span class="caption-text">Functional annotation workflow</span><a class="headerlink" href="#workflows-function-fig" title="Link to this image">#</a></p>
+</figcaption>
+</figure>
 <p>Functional annotation of <strong>metagenome-assembled genomes (MAGs)</strong> involves the identification and classification of genes
 within these reconstructed genomes to understand their roles and potential functions. MAGs are recovered from DNA directly
 extracted from complex microbial communities, bypassing the need to culture the organisms.</p>