update data summary slides

docs/articles/data_summary.html

@@ -10,7 +10,7 @@
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-  <title>Lee et al.&nbsp;(2023)</title>
+  <title>Data Summary</title>
   <meta name="apple-mobile-web-app-capable" content="yes">
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@@ -330,7 +330,7 @@
     <div class="slides">
 
 <section id="title-slide" class="quarto-title-block center">
-  <h1 class="title">Lee et al.&nbsp;(2023)</h1>
+  <h1 class="title">Data Summary</h1>
 
 <div class="quarto-title-authors">
 </div>
@@ -339,7 +339,7 @@ <h1 class="title">Lee et al.&nbsp;(2023)</h1>
 <section id="data-source" class="slide level2 smaller">
 <h2>Data Source</h2>
 
-<img data-src="images/Capture.PNG" class="r-stretch"><p>The data used comes from the study titled “Population-level impacts of antibiotic usage on the human gut microbiome”, published in Nature Communications in 2023 by Lee et al.&nbsp;This large-scale study includes a total of 9,251 samples collected from various human body sites and countries.</p>
+<img data-src="images/Capture.PNG" class="r-stretch"><p>This large-scale study includes a total of 9,251 samples collected from various human body sites and countries.</p>
 </section>
 <section id="aims-of-the-study" class="slide level2 smaller">
 <h2>Aims of the study</h2>
@@ -351,11 +351,17 @@ <h2>Aims of the study</h2>
 <section id="methods-data-collection-compilation" class="slide level2 smaller">
 <h2>Methods: Data Collection &amp; Compilation</h2>
 <ul>
-<li><p>Manually curated ARG families from CARD database (n=752)&nbsp; &nbsp;</p></li>
+<li><p><em>Raw Illumina sequencing reads from NCBI or EMBL using Kingfisher-download</em></p></li>
+<li><p>Metagenomic assemblies retrieved from <a href="http://segatalab.cibio.unitn.it/data/Pasolli_et_al.html">Pasolli et al.</a></p></li>
+</ul>
+<!-- -->
+<ul>
 <li><p>6104 adult gut metagenome samples from 20 countries after refinning</p></li>
 <li><p>curatedMetagenomeData R package for retrieving the sample metadata</p></li>
-<li><p>Raw Illumina sequencing reads from NCBI or EMBL using Kingfisher-download</p></li>
-<li><p>Metagenomic assemblies retrieved from <a href="http://segatalab.cibio.unitn.it/data/Pasolli_et_al.html">Pasolli et al.</a></p></li>
+</ul>
+<!-- -->
+<ul>
+<li>Manually curated ARG families from CARD database (n=752)&nbsp; &nbsp;</li>
 </ul>
 </section>
 <section id="original-data-sample-distribution" class="slide level2 smaller">
@@ -383,10 +389,13 @@ <h2>Original Data Sample Distribution</h2>
 <h2>Data Subsetting</h2>
 <p>The data has been carefully subsetted to include samples that meet specific criteria, such as:</p>
 <ul>
-<li><p><strong>SCGs:</strong> Selected samples with all <strong>40 Single-Copy Genes (SCGs)</strong> recovered (<code>Tier_2.Recover_all_40_SCGs</code>).</p></li>
 <li><p><strong>Body Site:</strong> Limited to <strong>stool samples</strong> (<code>BodySite</code>).</p></li>
-<li><p><strong>Age Category:</strong> Included only <strong>adult subjects</strong> (<code>AgeCategory</code>).</p></li>
 <li><p><strong>Health Status:</strong> Focused on <strong>healthy individuals</strong> not currently using antibiotics (<code>Disease</code> and <code>antibiotic_current_use_binary</code>).</p></li>
+<li><p><strong>Age Category:</strong> Included only <strong>adult subjects</strong> (<code>AgeCategory</code>).</p></li>
+</ul>
+<!-- -->
+<ul>
+<li><strong>SCGs:</strong> Selected samples with all <strong>40 Single-Copy Genes (SCGs)</strong> recovered</li>
 </ul>
 <p>This subset of the data, now represented as a <code>TreeSummarizedExperiment</code> (TSE) object, is optimized for further analysis and is available for advanced exploration of the antibiotic resistance gene (ARG) load, diversity, and related metadata.<br>
 To explore the metadata and access the object, visit <a href="https://github.com/microbiome/data/blob/main/Lee2023/README.md">this link</a>.</p>

docs/articles/data_summary.qmd

@@ -1,5 +1,5 @@
 ---
-title: Lee et al. (2023)
+title: Data Summary
 format: 
   revealjs:
     theme: white
@@ -14,7 +14,7 @@ format:
 
 ![](images/Capture.PNG)
 
-The data used comes from the study titled "Population-level impacts of antibiotic usage on the human gut microbiome", published in Nature Communications in 2023 by Lee et al. This large-scale study includes a total of 9,251 samples collected from various human body sites and countries.
+This large-scale study includes a total of 9,251 samples collected from various human body sites and countries.
 
 ## Aims of the study {.smaller}
 
@@ -24,15 +24,21 @@ The data used comes from the study titled "Population-level impacts of antibioti
 
 ## Methods: Data Collection & Compilation {.smaller}
 
--   Manually curated ARG families from CARD database (n=752)   
+-   *Raw Illumina sequencing reads from NCBI or EMBL using Kingfisher-download*
+
+-   Metagenomic assemblies retrieved from [Pasolli et al.](http://segatalab.cibio.unitn.it/data/Pasolli_et_al.html)
 
+```{=html}
+<!-- -->
+```
 -   6104 adult gut metagenome samples from 20 countries after refinning
 
 -   curatedMetagenomeData R package for retrieving the sample metadata
 
--   Raw Illumina sequencing reads from NCBI or EMBL using Kingfisher-download
-
--   Metagenomic assemblies retrieved from [Pasolli et al.](http://segatalab.cibio.unitn.it/data/Pasolli_et_al.html)
+```{=html}
+<!-- -->
+```
+-   Manually curated ARG families from CARD database (n=752)   
 
 ## Original Data Sample Distribution {.smaller}
 
@@ -132,18 +138,21 @@ ggplot(country_sample_data, aes(x = Number_of_Samples, y = Country)) +
 
 The data has been carefully subsetted to include samples that meet specific criteria, such as:
 
--   **SCGs:** Selected samples with all **40 Single-Copy Genes (SCGs)** recovered (`Tier_2.Recover_all_40_SCGs`).
-
 -   **Body Site:** Limited to **stool samples** (`BodySite`).
 
+-   **Health Status:** Focused on **healthy individuals** not currently using antibiotics (`Disease` and `antibiotic_current_use_binary`).
+
 -   **Age Category:** Included only **adult subjects** (`AgeCategory`).
 
--   **Health Status:** Focused on **healthy individuals** not currently using antibiotics (`Disease` and `antibiotic_current_use_binary`).
+```{=html}
+<!-- -->
+```
+-   **SCGs:** Selected samples with all **40 Single-Copy Genes (SCGs)** recovered
 
-This subset of the data, now represented as a `TreeSummarizedExperiment` (TSE) object, is optimized for further analysis and is available for advanced exploration of the antibiotic resistance gene (ARG) load, diversity, and related metadata. \
+This subset of the data, now represented as a `TreeSummarizedExperiment` (TSE) object, is optimized for further analysis and is available for advanced exploration of the antibiotic resistance gene (ARG) load, diversity, and related metadata.\
 To explore the metadata and access the object, visit [this link](https://github.com/microbiome/data/blob/main/Lee2023/README.md).
 
-## Sample Metadata  {.smaller}
+## Sample Metadata {.smaller}
 
 The subsetted dataset contains key metadata that provides context to each sample.
 
@@ -197,7 +206,7 @@ combined_summary_df %>%
 
 ```
 
-## Distribution of Sample Metadata  {.smaller}
+## Distribution of Sample Metadata {.smaller}
 
 ![](images/country.png)
 
@@ -223,7 +232,7 @@ combined_summary_df %>%
 
 ![](images/median_read_length.png)
 
-## NDARO Dataset  {.smaller}
+## NDARO Dataset {.smaller}
 
 NDARO is a collaborative, cross-agency, centralized hub for researchers to access AMR data to facilitate real-time surveillance of pathogenic organisms. NDARO is part of the National Action Plan for Combating Antibiotic-Resistant Bacteria developed by the White House in 2015.