formatting changes

Author: lper0012

Functiona_Enrichment.log

@@ -1,5 +1,5 @@
 # example R options set globally
-options(width = 60)
+options(width = 100)
 
 # example chunk options set globally
 knitr::opts_chunk$set(

Functiona_Enrichment.pdf

@@ -1,12 +1,14 @@
 bookdown::bs4_book:
+  include:
+    before_body: title.html
   css: style.css
   # includes:
   #   in_header: custom-header.html
   # before_body: custom.js
   # includes:
   #   in_header: custom.js
   theme:
-    primary: "#1D0F81"
+    primary: "green"
   repo: https://github.com/MonashBioinformaticsPlatfor/Functional_Enrichment_BioCommons_2024
   # toc_depth: 2  # Adjust the depth as needed (e.g., 2 for up to H2 headers)
 bookdown::pdf_book:
@@ -16,3 +18,12 @@ bookdown::pdf_book:
   citation_package: natbib
   keep_tex: yes
 bookdown::epub_book: default
+bookdown::gitbook:
+  css: style.css
+  config:
+    toc:
+      before: |
+        <a href="https://www.example.com/"><img src="Sydney_informatics_hub_logo.png" width="280"></a>
+        <li><a href="./">An example Resource</a></li>
+      after: |
+        <li><a href="https://github.com/rstudio/bookdown" target="blank">Published with bookdown</a></li>

Functiona_Enrichment.tex

@@ -1,6 +1,6 @@
 ---
 title: "Functional Enrichment Workshop"
-author: "Monash Genomics and Bioinformatics Platform (MGBP)"
+author: "Australian Biocommons, Sydney Informatics Hub (USYD) and Monash Genomics and Bioinformatics Platform (MGBP)"
 date: "Compiled: `r format(Sys.Date(), '%B %d, %Y')`"
 site: bookdown::bookdown_site
 output: bookdown::bs4_book
@@ -10,6 +10,8 @@ description: |
   A comprehensive guide to functional enrichment analysis using both online platforms and command-line tools.
 link-citations: yes
 github-repo: "https://github.com/MonashBioinformaticsPlatform/Functional_Enrichment_Workshop_2024"
+always_allow_html: true
+# cover-image: Sydney_informatics_hub_logo.png
 ---
 
 # Functional Enrichment Workshop

Sydney_informatics_hub_logo.png

@@ -1,7 +1,7 @@
 
 /* Adjust the width of the main content area */
 .book .book-body .body-inner {
-  max-width: 60%;
+  max-width: 100%;
   margin: auto;
 }
 

_common.R

@@ -0,0 +1 @@
+<span class="main-title"><em>Making sense of gene and proteins lists with functional enrichment analysis</em></span>