Merge pull request #42 from bcbio/devel

Upgrade to usethis functions

.github/workflows/R-CMD-check.yaml

@@ -18,9 +18,9 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macos-latest,   r: 'release'}
+          # - {os: macos-latest,   r: 'release'}
           #- {os: windows-latest, r: 'release'}
-          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          # - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
           #- {os: ubuntu-latest,   r: 'oldrel-1'}
 
@@ -47,4 +47,5 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          error-on: '"error"'
           build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.gitignore

@@ -13,3 +13,12 @@ docs
 /doc/
 /Meta/
 .DS*
+inst/rmarkdown/templates/rnaseq/skeleton/DE/Multiplicative_DGE_Analysis.Rmd
+.Rdata
+.httr-oauth
+.DS_Store
+.quarto
+inst/templates/chipseq/QC/QC.html
+*.html
+*.csv
+*.qs

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: bcbioR
 Type: Package
 Title: Templates and functions to guide downstream analysis and data interpretation
-Version: 0.1.3
+Version: 0.3.0
 Authors@R: person("Pantano", "Lorena", , "[email protected]",
             role = c("aut", "cre"))
 Description: Collaborative code repository at the Harvard Chan Bioinformatics Core.
@@ -11,23 +11,28 @@ Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
 Imports: 
-    DESeq2,
-    stringr,
-    ggplot2,
     magrittr,
-    hues,
-    ggprism,
     grDevices,
     R.utils,
     readr,
+    withr,
+    usethis,
     fs,
-    withr
+    jsonlite,
+    yaml,
+    whisker,
+    rlang,
+    stringr,
+    utils
 Suggests: 
+    hues,
+    ggprism,
+    ggplot2,
     knitr,
     rmarkdown,
     testthat (>= 3.0.0)
 VignetteBuilder: knitr
 URL: http://bcb.io/bcbioR/
 Config/testthat/edition: 3
 Depends: 
-    R (>= 2.10)
+    R (>= 4.2.0)

NAMESPACE

@@ -1,19 +1,20 @@
 # Generated by roxygen2: do not edit by hand
 
 export(bcbio_nfcore_check)
-export(bcbio_set_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(DESeq2)
 import(R.utils)
-import(ggplot2)
-import(ggprism)
-import(hues)
+import(fs)
+import(usethis)
+import(whisker)
+import(withr)
 importFrom(grDevices,colorRampPalette)
 importFrom(magrittr,"%>%")
 importFrom(readr,read_csv)
 importFrom(stringr,str_replace_all)
+importFrom(utils,download.file)
+importFrom(utils,unzip)

NEWS.md

@@ -1,3 +1,22 @@
+# bcbioR 0.3.0
+
+* re-structure templates
+* Add text with best practices
+* Reproducibility:
+  * test data for RNAseq, singlecell, CHIPseq
+* Base project:
+  * Guidelines to create repo easily
+  * Example Rmd with headers and aesthetics
+* RNASEQ
+  * Use provenance for FA in DE report
+  * Support multiple comparisons
+* New templates:
+  * methylation - draft
+  * singcell cell QC and Inegration - stable
+  * scQC shiny app - stable
+  * chipseq QC and Diffbind - beta
+  * COSMX - draft
+
 # bcbioR 0.1.3
 
 * fix duplicated gene names

R/bcbioR-package.R

@@ -6,10 +6,12 @@
 #' @importFrom magrittr %>%
 #' @importFrom readr read_csv
 #' @importFrom stringr str_replace_all
+#' @importFrom utils download.file
+#' @importFrom utils unzip
 ## usethis namespace: end
-#' @import DESeq2
-#' @import ggplot2
-#' @import hues
-#' @import ggprism
+#' @import usethis
+#' @import fs
 #' @import R.utils
+#' @import withr
+#' @import whisker
 NULL

R/cb_friendly.R

@@ -49,12 +49,13 @@ cb_friendly_palettes <- list(
   `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")
+  `heatmap` = cb_friendly_cols("blue", "white", "brown"),
+  `white_to_blue` = cb_friendly_cols('white', 'blue')
 )
 
 #' access cb friendly palette by name, reversing if necessary
 #'
-#' @param palette name of the palette to be returned
+#' @param palette name of the palette to be returned (main, cool, hot, grey, white_to_blue, or heatmap)
 #' @param reverse boolean, reverse order of colors in palette
 #' @param ... pass to ggplot
 #' @export
@@ -66,7 +67,7 @@ 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 palette name of the palette to be returned (main, cool, hot, grey, white_to_blue, or heatmap)
 #' @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
@@ -83,7 +84,7 @@ 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 palette name of the palette to be returned (main, cool, hot, grey, white_to_blue, or heatmap)
 #' @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