add vignette

.gitignore

@@ -5,4 +5,5 @@
 *.Rproj
 test/*
 inst/*/*/*/*/*/*html
-inst/*/*/*/*/*/*csv
+inst/*/*/*/*/*/*csv
+inst/doc

DESCRIPTION

@@ -14,3 +14,7 @@ Imports:
     stringr,
     ggplot2,
     magrittr
+Suggests: 
+    knitr,
+    rmarkdown
+VignetteBuilder: knitr

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)

R/bcbioR-package.R

@@ -6,4 +6,5 @@
 #' @importFrom stringr str_replace_all
 ## usethis namespace: end
 #' @import ggplot2
+#' @import hues
 NULL

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.

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`

vignettes/.gitignore

@@ -0,0 +1,2 @@
+*.html
+*.R

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))
+```
+