Merge pull request #14 from bcbio/devel

v0.1.1

.Rbuildignore

@@ -3,3 +3,11 @@
 ^\.github$
 ^README\.Rmd$
 ^LICENSE\.md$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^doc$
+^Meta$
+test/*
+inst/*/*/*/*/*/*html
+inst/*/*/*/*/*/*csv

.github/workflows/pkgdown.yaml

@@ -0,0 +1,48 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

@@ -5,4 +5,8 @@
 *.Rproj
 test/*
 inst/*/*/*/*/*/*html
-inst/*/*/*/*/*/*csv
+inst/*/*/*/*/*/*csv
+inst/doc
+docs
+/doc/
+/Meta/

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: bcbioR
 Type: Package
 Title: Templates and functions to guide downstream analysis and data interpretation
-Version: 0.1.0
+Version: 0.1.1
 Authors@R: person("Pantano", "Lorena", , "[email protected]",
             role = c("aut", "cre"))
 Description: Collaborative code repository at the Harvard Chan Bioinformatics Core.
@@ -13,4 +13,13 @@ RoxygenNote: 7.3.1
 Imports: 
     stringr,
     ggplot2,
-    magrittr
+    magrittr,
+    hues,
+    ggprism,
+    grDevices,
+    R.utils
+Suggests: 
+    knitr,
+    rmarkdown
+VignetteBuilder: knitr
+URL: http://bcb.io/bcbioR/

NAMESPACE

@@ -1,14 +1,16 @@
 # Generated by roxygen2: do not edit by hand
 
-export(bcbio_gitignore)
 export(bcbio_set_project)
-export(bcbio_start_project)
 export(bcbio_templates)
 export(cb_friendly_cols)
 export(cb_friendly_pal)
 export(list_cb_friendly_cols)
 export(scale_color_cb_friendly)
 export(scale_fill_cb_friendly)
+import(R.utils)
 import(ggplot2)
+import(ggprism)
+import(hues)
+importFrom(grDevices,colorRampPalette)
 importFrom(magrittr,"%>%")
 importFrom(stringr,str_replace_all)

NEWS.md

@@ -0,0 +1,5 @@
+# bcbioR 0.1.1
+
+* Add page to github
+* Make CHECK to pass
+* Add vignette

R/bcbioR-package.R

@@ -4,6 +4,10 @@
 ## usethis namespace: start
 #' @importFrom magrittr %>%
 #' @importFrom stringr str_replace_all
+#' @importFrom grDevices colorRampPalette
 ## usethis namespace: end
 #' @import ggplot2
+#' @import hues
+#' @import ggprism
+#' @import R.utils
 NULL

R/cb_friendly.R

@@ -1,15 +1,15 @@
 #' list of colorblind-friendly colors, developed by James and client
 cb_friendly_colors <- c(
   `blue`            = "#2759F6",
-  `dark_purple`     = "#402999",
+  `light_orange`    = "#FFD37D",
+  `olive_green`     = "olivedrab3",
   `purple`          = "#9176C8",
+  `pink`            = "#E93380",
   `sky_blue`        = "#4FAEEB",
   `blue_grey`       = "#92A6BC",
   `forest_green`    = "#3C877B",
-  `pink`            = "#E93380",
-  `olive_green`     = "olivedrab3",
   `yellow`          = "yellow",
-  `light_orange`    = "#FFD37D",
+  `dark_purple`     = "#402999",
   `dark_orange`     = "#D5392C",
   `army_green`      = "#C3C380",
   `black`           = "black",
@@ -26,33 +26,37 @@ list_cb_friendly_cols <- function(){
 }
 
 #' fetch color from list by name
+#'
+#' @param ... list of color names
+#'
 #' @export
 cb_friendly_cols <- function(...) {
   cols <- c(...)
-  
+
   if (is.null(cols))
     return (cb_friendly_colors)
-  
+
   cb_friendly_colors[cols]
 }
 
 #' define main colorblind-friendly palette as well as sub-palettes
 cb_friendly_palettes <- list(
-  `main`  = cb_friendly_cols("blue", "dark_purple", "purple", "sky_blue", 
-                               "blue_grey", "forest_green", "pink", "olive_green", 
-                               "yellow", "light_orange", "dark_orange",
-                               "army_green", "black", "dark_grey", "light_blue", 
-                               "brown"),
+  `main`  = cb_friendly_cols("blue", "purple", "sky_blue",
+                               "blue_grey", "forest_green", "pink", "olive_green",
+                               "yellow", "dark_purple", "dark_orange",
+                               "army_green", "black", "dark_grey", "light_blue",
+                               "brown","light_orange"),
   `cool`  = cb_friendly_cols("blue", "dark_purple", "purple", "sky_blue"),
   `hot`   = cb_friendly_cols("yellow", "light_orange", "dark_orange"),
   `grey`  = cb_friendly_cols("black", "dark_grey", "blue_grey"),
   `heatmap` = cb_friendly_cols("blue", "white", "brown")
 )
 
 #' access cb friendly palette by name, reversing if necessary
-#' 
+#'
 #' @param palette name of the palette to be returned
 #' @param reverse boolean, reverse order of colors in palette
+#' @param ... pass to ggplot
 #' @export
 cb_friendly_pal <-function(palette = 'main', reverse = F, ...){
   pal <- cb_friendly_palettes[[palette]]
@@ -61,14 +65,15 @@ cb_friendly_pal <-function(palette = 'main', reverse = F, ...){
 }
 
 #' use cb friendly colors as color aesthetic with ggplot
-#' 
+#'
 #' @param palette name of the palette to be returned
 #' @param discrete boolean, whether to make palette discretely divided into colors or continuous
 #' @param reverse boolean, reverse order of colors in palette
+#' @param ... pass to ggplot
 #' @export
 scale_color_cb_friendly <- function(palette = "main", discrete = TRUE, reverse = FALSE, ...) {
   pal <- cb_friendly_pal(palette = palette, reverse = reverse)
-  
+
   if (discrete) {
     discrete_scale("colour", paste0("cb_friendly_", palette), palette = pal, ...)
   } else {
@@ -77,17 +82,18 @@ scale_color_cb_friendly <- function(palette = "main", discrete = TRUE, reverse =
 }
 
 #' use cb friendly colors as fill aesthetic with ggplot
-#' 
+#'
 #' @param palette name of the palette to be returned
 #' @param discrete boolean, whether to make palette discretely divided into colors or continuous
 #' @param reverse boolean, reverse order of colors in palette
+#' @param ... pass to ggplot
 #' @export
 scale_fill_cb_friendly <- function(palette = "main", discrete = TRUE, reverse = FALSE, ...) {
   pal <- cb_friendly_pal(palette = palette, reverse = reverse)
-  
+
   if (discrete) {
     discrete_scale("fill", paste0("cb_friendly_", palette), palette = pal, ...)
   } else {
     scale_fill_gradientn(colours = pal(256), ...)
   }
-}
+}

R/hello.R

@@ -27,13 +27,13 @@ bcbio_templates <- function(type="rnaseq", outpath){
 
            fpath <- system.file("rmarkdown/templates/rnaseq", "skeleton", package="bcbioR")
            #file.copy(fpath, outpath, recursive = T)
-           R.utils::copyDirectory(fpath, outpath)
+           copyDirectory(fpath, outpath)
          },
          scrnaseq={
 
            fpath <- system.file("rmarkdown/templates/singlecell", "skeleton", package="bcbioR")
            #file.copy(fpath, outpath, recursive = T)
-           R.utils::copyDirectory(fpath, outpath)
+           copyDirectory(fpath, outpath)
          },
          {
            stop('project type not recognize, please choose: ', 'rnaseq', 'scrnaseq')
@@ -76,12 +76,11 @@ bcbio_set_project <- function() {
   return(opts)
 }
 
-#' @export
+
 bcbio_start_project <- function(options) {
 
 }
 
-#' @export
 bcbio_gitignore <- function(options) {
 
 }

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`

_pkgdown.yml

@@ -0,0 +1,4 @@
+url: http://bcb.io/bcbioR/
+template:
+  bootstrap: 5
+