From eee90db13d892617d82fe935fbf96c5867fca406 Mon Sep 17 00:00:00 2001
From: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>
Date: Wed, 2 Apr 2025 17:30:14 -0400
Subject: [PATCH 1/4] add vignette builder

---
 example.R          |  8 --------
 vignettes/demo.Rmd | 11 ++++++++---
 2 files changed, 8 insertions(+), 11 deletions(-)
 delete mode 100644 example.R

diff --git a/example.R b/example.R
deleted file mode 100644
index ac5bef5..0000000
--- a/example.R
+++ /dev/null
@@ -1,8 +0,0 @@
-library(NetworkDataCompanion)
-
-
-#create object from NetworkDataCompanion class
-obj <- CreateNetworkDataCompanionObject(argument_one = "hehehe")
-
-
-obj$convertBetaToM
\ No newline at end of file
diff --git a/vignettes/demo.Rmd b/vignettes/demo.Rmd
index 4f02064..d68f445 100644
--- a/vignettes/demo.Rmd
+++ b/vignettes/demo.Rmd
@@ -9,6 +9,11 @@ bibliography: demo.bib
 link-citations: true
 ---
 
+<!--
+%\VignetteEngine{knitr::rmarkdown}
+%\VignetteIndexEntry{Demo}
+-->
+
 # About NetworkDataCompanion
 
 The `NetworkDataCompanion` R package is a collection of utilities for wrangling TCGA data. While it was developed to serve as the engine behind `tcga-data-nf`, the Nextflow workflow presented in @fanfani2024reproducible, `NetworkDataCompanion` is a stand-alone package that can be used independently. The primary goal of the package is to provide version-controlled and unit-tested functions for common tasks involved in network analyses of TCGA data, such as calculating gene-level summary measures of methylation data, normalizing RNA-seq data, and integrating multiple omics by mapping various file identifiers back to TCGA barcodes. 
@@ -21,14 +26,14 @@ While none of these tasks are particularly complex, `NetworkDataCompanion` is mo
 
 # Preparing the workspace
 
-The first step is to install `NetworkDataCompanion` from GitHub using the `devtools` library and the `install_github` function.
+The first step is to install `NetworkDataCompanion` from GitHub using the `devtools` library and the `install_github` function. Here, we have suppressed messages as there are quite a few. 
 
-```{R}
+```{R, message=F}
 library(devtools)
 devtools::install_github("QuackenbushLab/NetworkDataCompanion")
 ```
 
-Once you have installed the package, load the library into your workspace. Here, we have suppressed package loading messages as there are quite a few. 
+Once you have installed the package, load the library into your workspace. 
 
 ```{R, message=F}
 library(NetworkDataCompanion)

From e4bded3bd64186ac3691f9230359aa5a114a0fa1 Mon Sep 17 00:00:00 2001
From: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>
Date: Wed, 2 Apr 2025 20:07:47 -0400
Subject: [PATCH 2/4] add rmdformats for vignette

---
 DESCRIPTION | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 5e79fd5..6183809 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -47,5 +47,6 @@ Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
 Suggests: 
     knitr,
-    rmarkdown
+    rmarkdown,
+    rmdformats
 VignetteBuilder: knitr

From 4c1510e28b1afeb11e1f9629586e00e08baa4aa3 Mon Sep 17 00:00:00 2001
From: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>
Date: Wed, 2 Apr 2025 20:17:07 -0400
Subject: [PATCH 3/4] added devtools

---
 DESCRIPTION | 1 +
 1 file changed, 1 insertion(+)

diff --git a/DESCRIPTION b/DESCRIPTION
index 6183809..2f0dffa 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -46,6 +46,7 @@ Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
 Suggests: 
+    devtools,
     knitr,
     rmarkdown,
     rmdformats

From c14abb5f5999554c5f97f8fcff3a3e7c3c215222 Mon Sep 17 00:00:00 2001
From: katehoffshutta <43797774+katehoffshutta@users.noreply.github.com>
Date: Thu, 3 Apr 2025 21:04:39 -0400
Subject: [PATCH 4/4] moved demo out of vignettes

---
 vignettes/demo.Rmd => quickstart.Rmd | 7 +------
 vignettes/demo.bib => quickstart.bib | 0
 2 files changed, 1 insertion(+), 6 deletions(-)
 rename vignettes/demo.Rmd => quickstart.Rmd (98%)
 rename vignettes/demo.bib => quickstart.bib (100%)

diff --git a/vignettes/demo.Rmd b/quickstart.Rmd
similarity index 98%
rename from vignettes/demo.Rmd
rename to quickstart.Rmd
index d68f445..7791dfc 100644
--- a/vignettes/demo.Rmd
+++ b/quickstart.Rmd
@@ -5,15 +5,10 @@ output:
   rmdformats::robobook:
     code_folding: show
     toc_depth: 4
-bibliography: demo.bib  
+bibliography: quickstart.bib  
 link-citations: true
 ---
 
-<!--
-%\VignetteEngine{knitr::rmarkdown}
-%\VignetteIndexEntry{Demo}
--->
-
 # About NetworkDataCompanion
 
 The `NetworkDataCompanion` R package is a collection of utilities for wrangling TCGA data. While it was developed to serve as the engine behind `tcga-data-nf`, the Nextflow workflow presented in @fanfani2024reproducible, `NetworkDataCompanion` is a stand-alone package that can be used independently. The primary goal of the package is to provide version-controlled and unit-tested functions for common tasks involved in network analyses of TCGA data, such as calculating gene-level summary measures of methylation data, normalizing RNA-seq data, and integrating multiple omics by mapping various file identifiers back to TCGA barcodes. 
diff --git a/vignettes/demo.bib b/quickstart.bib
similarity index 100%
rename from vignettes/demo.bib
rename to quickstart.bib