Merge pull request #30 from bcbio/devel

0.2.1

.Rbuildignore

@@ -11,3 +11,4 @@
 test/*
 inst/*/*/*/*/*/*html
 inst/*/*/*/*/*/*csv
+^data-raw$

.gitignore

@@ -10,3 +10,4 @@ inst/doc
 docs
 /doc/
 /Meta/
+.DS*

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: bcbioR
 Type: Package
 Title: Templates and functions to guide downstream analysis and data interpretation
-Version: 0.1.1
+Version: 0.1.2
 Authors@R: person("Pantano", "Lorena", , "[email protected]",
             role = c("aut", "cre"))
 Description: Collaborative code repository at the Harvard Chan Bioinformatics Core.
@@ -11,15 +11,23 @@ Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
 Imports: 
+    DESeq2,
     stringr,
     ggplot2,
     magrittr,
     hues,
     ggprism,
     grDevices,
-    R.utils
+    R.utils,
+    readr,
+    fs,
+    withr
 Suggests: 
     knitr,
-    rmarkdown
+    rmarkdown,
+    testthat (>= 3.0.0)
 VignetteBuilder: knitr
 URL: http://bcb.io/bcbioR/
+Config/testthat/edition: 3
+Depends: 
+    R (>= 2.10)

NAMESPACE

@@ -1,16 +1,19 @@
 # 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)
 importFrom(grDevices,colorRampPalette)
 importFrom(magrittr,"%>%")
+importFrom(readr,read_csv)
 importFrom(stringr,str_replace_all)

NEWS.md

@@ -1,3 +1,15 @@
+# bcbioR 0.1.2
+
+* Add draft templates for TEAseq, COSMX
+* Adapt templates to nf-core rnaseq
+* Fix when sample start by number
+* Fix when rRNA rate is missing
+* Add by sample plots in QC
+* Add function to check nfcore samplesheet
+* Add PCA with variance analysis
+* Minor details fixed in QC RNAseq report
+* Correct metric for rRNA and tRNA
+
 # bcbioR 0.1.1
 
 * Add page to github

R/bcbioR-package.R

@@ -2,10 +2,12 @@
 "_PACKAGE"
 
 ## usethis namespace: start
+#' @importFrom grDevices colorRampPalette
 #' @importFrom magrittr %>%
+#' @importFrom readr read_csv
 #' @importFrom stringr str_replace_all
-#' @importFrom grDevices colorRampPalette
 ## usethis namespace: end
+#' @import DESeq2
 #' @import ggplot2
 #' @import hues
 #' @import ggprism

R/data.R

@@ -0,0 +1,8 @@
+#' varianceStabilizingTransformation Object from Test Data
+#'
+#' An example of the output of varianceStabilizingTransformation to
+#' show different visualization code
+#'
+#' @format ## `bcbio_vsd_data`
+#' VSD object from DESeq2 data
+"bcbio_vsd_data"

R/hello.R

@@ -1,8 +1,34 @@
 .fix <- function(x){
   x <- tolower(x) %>% str_replace_all(., "[[:punct:]]", "_")
+  x <- str_replace_all(x, " ", "_")
   return(x)
 }
 
+
+#' Function to check samplesheet for nf-core
+#'
+#' @param file path to CSV file for nf-core
+#' @examples
+#'
+#' bcbio_nfcore_check(system.file("extdata", "rnaseq_good.csv", package = "bcbioR") )
+#'
+#' @export
+bcbio_nfcore_check <- function(file){
+  required=c("sample","fastq_1","fastq_2","strandedness")
+  samplesheet=read_csv(file)
+
+  if (!(all(required %in% colnames(samplesheet)))){
+    print(colnames(samplesheet))
+    stop("Missing required columns ", paste(required, collapse = " "))
+  }else if (any(grepl("^[1-9]", samplesheet[["sample"]]))){
+    stop("Avoid samples starting with numbers ")
+  }else if (any(is.na(samplesheet))){
+    warning("Columns with missing values")
+  }else{
+    message("All good.")
+  }
+}
+
 #' Function to help deploy analysis folder inside a project folder
 #'
 #' This function contains Rmd, R, md, files that help to structure
@@ -13,7 +39,11 @@
 #' Normally these helper files are inside a report folder inside a
 #' project folder.
 #'
-#' @param type string indicating the type of analysis, supported: rnaseq.
+#' @param type string indicating the type of analysis, supported:
+#'   - base
+#'   - rnaseq, scrnaseq,
+#'   - teaseq
+#'   - cosmx
 #'
 #' @param outpath string path indicating where to copy all the files to
 #' @examples
@@ -23,20 +53,30 @@
 #' @export
 bcbio_templates <- function(type="rnaseq", outpath){
   switch(type,
+         base={
+           fpath <- system.file("rmarkdown/templates/common", "skeleton", package="bcbioR")
+           copyDirectory(fpath, outpath)
+         },
          rnaseq={
-
            fpath <- system.file("rmarkdown/templates/rnaseq", "skeleton", package="bcbioR")
-           #file.copy(fpath, outpath, recursive = T)
            copyDirectory(fpath, outpath)
          },
          scrnaseq={
-
            fpath <- system.file("rmarkdown/templates/singlecell", "skeleton", package="bcbioR")
-           #file.copy(fpath, outpath, recursive = T)
+           copyDirectory(fpath, outpath)
+         },
+         teaseq={
+           fpath <- system.file("rmarkdown/templates/teaseq", "skeleton", package="bcbioR")
+           copyDirectory(fpath, outpath)
+         },
+         cosmx={
+           fpath <- system.file("rmarkdown/templates/cosmx", "skeleton", package="bcbioR")
            copyDirectory(fpath, outpath)
          },
          {
-           stop('project type not recognize, please choose: ', 'rnaseq', 'scrnaseq')
+           stop('project type not recognize, please choose: ', 'base',
+                'rnaseq', 'scrnaseq',
+                'teaseq', 'cosmx')
          }
   )
 }

README.md

@@ -1,28 +1,28 @@
-
 # bcbioR
 
 <!-- badges: start -->
 
 [![R-CMD-check](https://github.com/bcbio/bcbioR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/bcbio/bcbioR/actions/workflows/R-CMD-check.yaml)
+
 <!-- badges: end -->
 
-The goal of `bcbioR` is to create guidelines for NGS data interpretation
-based on the experience of the Harvard Chan Bioinformatics Core and
-everybody who contributes to this package.
+The goal of `bcbioR` is to create guidelines for NGS data interpretation based on the experience of the Harvard Chan Bioinformatics Core and everybody who contributes to this package.
 
 ## Installation
 
-You can install the development version of bcbioR from
-[GitHub](https://github.com/) with:
+You can install the development version of bcbioR from [GitHub](https://github.com/) with:
 
-``` r
+```         
 # install.packages("devtools")
 devtools::install_github("bcbio/bcbioR")
+devtools::install_github("bcbio/bcbioR",ref = "devel")
 ```
 
 ## Quick start
 
-``` r
+Use this code to generate a standard project name for all of your folders. **This code will not create any folders or files.**
+
+```
 library(bcbioR)
 ## basic example code
 # will help you to build a folder name following HCBC naming rules
@@ -31,46 +31,59 @@ bcbio_set_project()
 
 ### Set base project
 
-The following code will pop up a Rmd template and then clicking ‘save’
-will populate that folder with HCBC data structure guidelines
+use `setwd()` to set your current directory to the place where you want to work. The bcbioR functions will automatically write to whatever directory you have set.
 
-``` r
-rmarkdown::draft("project_folder",template="common",package="bcbioR")
+```
+setwd("/path/to/analysis/folder")
 ```
 
-As well, You can get this by going to File -\> New File -\> R
-markdown: - then `From Template`, and choose `bcbio base` - choose the
-folder to deploy files, it could be a new folder or an existing one
+The following code will pop up a Rmd template will populate that folder with HCBC data structure guidelines
+
+```
+bcbio_templates(type="base", outpath="/path/to/analysis/folder")
+```
 
 ### Set RNAseq report folder
 
-This code will populate the folder with HCBC data structure guidelines
-and Rmd code:
+This code will populate the folder with HCBC data structure guidelines and Rmd code: **You do not need to create a reports folder prior to running this code. This will create and populate the reports folder.**
 
-``` r
-bcbio_templates(type="rnaseq", outpath="test_folder/reports")
+``` 
+bcbio_templates(type="rnaseq", outpath="/path/to/analysis/folder/reports")
 ```
 
 ### Discover more…
 
-Go to the vignette to know more
-`vignette("bcbioR_quick_start,package="bcbioR")`
+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.
+### Open an issue
+
+-   If you find a bug
+-   If you want a new feature
+-   If you want to add code to the templates
+
+### Modify the code
+
+-   Clone the repository
+-   Make sure you are in the `devel` branch
+-   Create a new branch `git checkout -b feature1`
+-   Modify you code, add and commit
+-   Push to GitHub the new branch
+-   Create a PR from your branch to `devel`
+-   Assignt the PR to me or Alex
 
-Use `usethis::use_import_from("stringr","str_replace_all")` to add a
-function you are using in the code.
+Some best practices when developing:
 
-Don’t forget to commit and push the resulting figure files, so they
-display on GitHub and CRAN.
+-   install `devtools`
+-   Use `usethis::use_import_from("stringr","str_replace_all")` to add a new function you are using in the code.
 
 ### Contributors
 
-- Lorena Pantano
-- Alex Bartlett
-- Emma Berdan
-- Heather Wick
-- James Billingsley
+-   Lorena Pantano
+-   Alex Bartlett
+-   Emma Berdan
+-   Heather Wick
+-   James Billingsley
+-   Zhu Zhuo
+-   Elizabeth Partan