Merge pull request #52 from bcbio/devel

downgrade to warning minor version

Author: lpantano

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: bcbioR
 Type: Package
 Title: Templates and functions to guide downstream analysis and data interpretation
-Version: 0.3.0
+Version: 0.3.1
 Authors@R: person("Pantano", "Lorena", , "lorena.pantano@gmail.com",
             role = c("aut", "cre"))
 Description: Collaborative code repository at the Harvard Chan Bioinformatics Core.

NAMESPACE

@@ -7,6 +7,7 @@ export(cb_friendly_pal)
 export(list_cb_friendly_cols)
 export(scale_color_cb_friendly)
 export(scale_fill_cb_friendly)
+export(use_library)
 import(R.utils)
 import(fs)
 import(usethis)

NEWS.md

@@ -1,3 +1,8 @@
+# bcbioR 0.3.1
+
+- Fix bugs in RNAseq
+- Add function to set up library
+
 # bcbioR 0.3.0
 
 * re-structure templates

R/helpers.R

@@ -251,6 +251,29 @@ bcbio_render <- function(path, pipeline, data){
   }
 }
 
+
+#' Set custom library to your project
+#'
+#' This function will create the .Rprofile file in a project path
+#' to use a custom library path for future session
+#' @param custom_lib_path path with a R library folder
+#' @param project_path project path
+#' @examples
+#' path <- withr::local_tempdir()
+#' use_library(.libPaths(), path)
+#' @export
+use_library <- function(custom_lib_path, project_path="."){
+  # Path to your project's .Rprofile file
+  project_path <- fs::path_abs(project_path)
+  ui_info("Using this project path: {project_path}")
+  rprofile_path <- file.path(project_path, ".Rprofile")
+  # Command to set the library path
+  lib_path_command <- sprintf('.libPaths("%s")\n', custom_lib_path)
+  # Write the command to .Rprofile
+  writeLines(lib_path_command, con = rprofile_path)
+  source(rprofile_path)
+}
+
 # help with bcbio analysis setup
 use_bcbio_analysis <- function(path, pipeline, copy=TRUE, metadata=NULL){
 

README.md

@@ -1,11 +1,7 @@
 # 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.
 
 ## Installation
@@ -24,13 +20,13 @@ devtools::install_github("bcbio/bcbioR",ref = "devel")
 
 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.
 
-```
+```         
 setwd("/path/to/analysis/folder")
 ```
 
 The following code will pop up a Rmd template will populate that folder with HCBC data structure guidelines
 
-```
+```         
 path="/path/to/analysis/folder"
 bcbio_templates(type="base", outpath=path)
 bcbio_templates(type="rnaseq", outpath=path)
@@ -41,10 +37,27 @@ bcbio_templates(type="singlecell", outpath=path)
 
 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.**
 
-``` 
+```         
 bcbio_templates(type="rnaseq", outpath="/path/to/analysis/folder/reports")
 ```
 
+## Supported analyses
+
+-   base/reports/example.Rmd: ![](https://img.shields.io/badge/status-stable-green)
+-   rnaseq/DE/Intersections.Rmd: ![](https://img.shields.io/badge/status-alpha-yellow)
+-   rnaseq/DE/GSVA.Rmd: ![](https://img.shields.io/badge/status-alpha-yellow)
+-   rnaseq/DE/DEG.Rmd: ![](https://img.shields.io/badge/status-stable-green)
+-   rnaseq/DE/Cross-comparison-analysis.Rmd: ![](https://img.shields.io/badge/status-alpha-yellow)
+-   rnaseq/QC/QC_nf-core.Rmd: ![](https://img.shields.io/badge/status-stable-green)
+-   singlecell/Integration/norm_integration.rmd: ![](https://img.shields.io/badge/status-alpha-yellow)
+-   singlecell/QC/QC.rmd: ![](https://img.shields.io/badge/status-alpha-yellow)
+-   singlecell_delux/CellToCell/cellchat.Rmd: ![](https://img.shields.io/badge/status-draft-grey)
+-   chipseq/diffbind/diffbind.Rmd: ![](https://img.shields.io/badge/status-alpha-yellow)
+-   chipseq/QC/QC.Rmd: ![](https://img.shields.io/badge/status-alpha-yellow)
+-   spatial/cosmx/QC/QC.Rmd: ![](https://img.shields.io/badge/status-draft-grey)
+-   methylation/QC/QC.Rmd: ![](https://img.shields.io/badge/status-draft-grey)
+-   multiomics/teaseq/QC/QC.Rmd: ![](https://img.shields.io/badge/status-draft-grey)
+
 ### Discover more…
 
 Go to the vignette to know more `vignette("bcbioR_quick_start", package="bcbioR")`

inst/templates/base/reports/example.Rmd

@@ -27,7 +27,7 @@ setwd(fs::path_dir(getSourceEditorContext()$path))
 # NOTE: This code will check version, this is our recommendation, it may work
 #.      other versions
 stopifnot(R.version$major>= 4) # requires R4
-stopifnot(compareVersion(R.version$minor,"3.3")==0) # requires >=4.3.3
+if (compareVersion(R.version$minor,"3.1")<0) warning("We recommend >= R4.3.1") 
 stopifnot(compareVersion(as.character(BiocManager::version()), "3.18")>=0)
 ```
 
@@ -76,3 +76,11 @@ opts_chunk[["set"]](
 -   PI: `r PI`
 -   Analyst: `r analyst`
 -   Experiment: `r experiment`
+
+# R session
+
+List and version of tools used for the QC report generation.
+
+```{r}
+sessionInfo()
+```

inst/templates/chipseq/QC/QC.Rmd

@@ -33,7 +33,7 @@ setwd(fs::path_dir(getSourceEditorContext()$path))
 # NOTE: This code will check version, this is our recommendation, it may work
 #.      other versions
 stopifnot(R.version$major>= 4) # requires R4
-stopifnot(compareVersion(R.version$minor,"3.3")>=0) # requires >=4.3.3
+if (compareVersion(R.version$minor,"3.1")<0) warning("We recommend >= R4.3.1") 
 stopifnot(compareVersion(as.character(BiocManager::version()), "3.18")>=0)
 ```
 

inst/templates/chipseq/diffbind/diffbind.Rmd

@@ -40,7 +40,7 @@ setwd(fs::path_dir(getSourceEditorContext()$path))
 # NOTE: This code will check version, this is our recommendation, it may work
 #.      other versions
 stopifnot(R.version$major>= 4) # requires R4
-stopifnot(compareVersion(R.version$minor,"3.3")>=0) # requires >=4.3.3
+if (compareVersion(R.version$minor,"3.1")<0) warning("We recommend >= R4.3.1") 
 stopifnot(compareVersion(as.character(BiocManager::version()), "3.18")>=0)
 ```
 

inst/templates/methylation/QC/QC.Rmd

@@ -28,7 +28,7 @@ setwd(fs::path_dir(getSourceEditorContext()$path))
 # NOTE: This code will check version, this is our recommendation, it may work
 #.      other versions
 stopifnot(R.version$major>= 4) # requires R4
-stopifnot(compareVersion(R.version$minor,"3.3")==0) # requires >=4.3.3
+if (compareVersion(R.version$minor,"3.1")<0) warning("We recommend >= R4.3.1") 
 stopifnot(compareVersion(BiocManager::version(), "3.18")>=0)
 ```
 

inst/templates/rnaseq/DE/Cross-comparison-analysis.Rmd

@@ -27,7 +27,7 @@ setwd(fs::path_dir(getSourceEditorContext()$path))
 # NOTE: This code will check version, this is our recommendation, it may work
 #.      other versions
 stopifnot(R.version$major>= 4) # requires R4
-stopifnot(compareVersion(R.version$minor,"3.3")==0) # requires >=4.3.3
+if (compareVersion(R.version$minor,"3.1")<0) warning("We recommend >= R4.3.1") 
 stopifnot(compareVersion(as.character(BiocManager::version()), "3.18")>=0)
 ```
 
@@ -178,7 +178,7 @@ ggplot(lfc, aes(x=comp1, y=comp2, color=col)) + geom_point() +
 ```
 
 
-## Compare ajusted P-values
+## Compare adjusted P-values
 
 We plot adjusted P-values for our contrasts and color points by whether or not they are significant in our contrasts. The black line is 1:1.