From 492d9c99350acb4584dff9fb8602dd3c4dfe061c Mon Sep 17 00:00:00 2001
From: Lorena Pantano <lorena.pantano@gmail.com>
Date: Mon, 29 Apr 2024 17:16:10 -0400
Subject: [PATCH] add vignette

---
 .gitignore                       |  3 ++-
 DESCRIPTION                      |  4 +++
 NAMESPACE                        |  1 +
 R/bcbioR-package.R               |  1 +
 README.Rmd                       |  4 +++
 README.md                        |  5 ++++
 man/hello.Rd                     | 12 ---------
 vignettes/.gitignore             |  2 ++
 vignettes/bcbioR_quick_start.Rmd | 44 ++++++++++++++++++++++++++++++++
 9 files changed, 63 insertions(+), 13 deletions(-)
 delete mode 100644 man/hello.Rd
 create mode 100644 vignettes/.gitignore
 create mode 100644 vignettes/bcbioR_quick_start.Rmd

diff --git a/.gitignore b/.gitignore
index 7ae9725..6e74615 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,4 +5,5 @@
 *.Rproj
 test/*
 inst/*/*/*/*/*/*html
-inst/*/*/*/*/*/*csv
\ No newline at end of file
+inst/*/*/*/*/*/*csv
+inst/doc
diff --git a/DESCRIPTION b/DESCRIPTION
index 70ed6df..975ef50 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -14,3 +14,7 @@ Imports:
     stringr,
     ggplot2,
     magrittr
+Suggests: 
+    knitr,
+    rmarkdown
+VignetteBuilder: knitr
diff --git a/NAMESPACE b/NAMESPACE
index dafe89b..eb74e87 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -10,5 +10,6 @@ export(list_cb_friendly_cols)
 export(scale_color_cb_friendly)
 export(scale_fill_cb_friendly)
 import(ggplot2)
+import(hues)
 importFrom(magrittr,"%>%")
 importFrom(stringr,str_replace_all)
diff --git a/R/bcbioR-package.R b/R/bcbioR-package.R
index 611ed90..620ae89 100644
--- a/R/bcbioR-package.R
+++ b/R/bcbioR-package.R
@@ -6,4 +6,5 @@
 #' @importFrom stringr str_replace_all
 ## usethis namespace: end
 #' @import ggplot2
+#' @import hues
 NULL
diff --git a/README.Rmd b/README.Rmd
index 5b30416..b673c36 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -46,6 +46,10 @@ This code will populate the folder with HCBC data structure guidelines and Rmd c
 bcbio_templates(type="rnaseq", outpath="test_folder/reports")
 ```
 
+### Discover more
+
+Go to the vignette to know more `vignette("bcbioR_quick_start,package="bcbioR")`
+
 ## How to Contribute
 
 You'll still need to render `README.Rmd` regularly, to keep `README.md` up-to-date. `devtools::build_readme()` is handy for this.
diff --git a/README.md b/README.md
index df83c75..1ebc661 100644
--- a/README.md
+++ b/README.md
@@ -51,6 +51,11 @@ and Rmd code:
 bcbio_templates(type="rnaseq", outpath="test_folder/reports")
 ```
 
+### Discover more
+
+Go to the vignette to know more
+`vignette("bcbioR_quick_start,package="bcbioR")`
+
 ## How to Contribute
 
 You’ll still need to render `README.Rmd` regularly, to keep `README.md`
diff --git a/man/hello.Rd b/man/hello.Rd
deleted file mode 100644
index 0fa7c4b..0000000
--- a/man/hello.Rd
+++ /dev/null
@@ -1,12 +0,0 @@
-\name{hello}
-\alias{hello}
-\title{Hello, World!}
-\usage{
-hello()
-}
-\description{
-Prints 'Hello, world!'.
-}
-\examples{
-hello()
-}
diff --git a/vignettes/.gitignore b/vignettes/.gitignore
new file mode 100644
index 0000000..097b241
--- /dev/null
+++ b/vignettes/.gitignore
@@ -0,0 +1,2 @@
+*.html
+*.R
diff --git a/vignettes/bcbioR_quick_start.Rmd b/vignettes/bcbioR_quick_start.Rmd
new file mode 100644
index 0000000..072ee90
--- /dev/null
+++ b/vignettes/bcbioR_quick_start.Rmd
@@ -0,0 +1,44 @@
+---
+title: "bcbioR quick start"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{Quick_Start}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+```
+
+```{r setup}
+library(bcbioR)
+library(ggplot2)
+```
+
+# Color blind friendly palette
+
+Compatible with `ggplot`.
+
+```{r}
+set.seed(596)
+dsamp <- diamonds[sample(nrow(diamonds), 1000), ]
+(d <- ggplot(dsamp, aes(carat, price)) +
+  geom_point(aes(colour = clarity)))
+d + scale_color_cb_friendly()
+```
+
+
+And get the colors directly:
+
+```{r}
+cb_friendly_cols(1:16)
+```
+```{r}
+library(hues)
+swatch(cb_friendly_cols(1:16))
+```
+