Merge pull request #52 from bcbio/devel

downgrade to warning minor version

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", , "[email protected]",
             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.
 

inst/templates/rnaseq/DE/DEG.Rmd

@@ -21,11 +21,11 @@ params:
   # numerator: tumor
   # denominator: normal
   column: "sample_type"
-  contrasts: !r list(c("sample_type", "tumor", "normal"))
+  contrasts: !r list(c("sample_type", "tumor", "normal"),c("sample_type", "normal", "tumor"))
   subset_column: null
   subset_value: null
   genome: hg38
-  ruv: true
+  ruv: false
   combatseq: false
   params_file: params_de-example.R
   project_file: ../information.R
@@ -41,7 +41,7 @@ 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)
 ```
 
@@ -58,9 +58,10 @@ map(list.files(params$functions_file,pattern = "*.R$",full.names = T), source) %
 # IMPORTANT set these values if you are not using the parameters in the header (lines 22-31)
 genome=params$genome
 column=params$column
+# use contrast to set up multiple comparisons
+# this is set up in the top as well, but you can change it here:
+# example would be: list(c("sample_type", "tumor", "normal"))
 contrasts=params$contrasts
-# numerator=params$numerator
-# denominator=params$denominator
 subset_column=params$subset_column
 subset_value=params$subset_value
 run_ruv=params$ruv
@@ -197,7 +198,7 @@ pca <- degPCA(norm_matrix, metrics,
 
 pca$plot + ggtitle(paste0("All samples", "\nPCA using ", nrow(vsd_before), " genes")) +
   theme(plot.title=element_text(hjust=0.5)) +
-  geom_mark_ellipse(aes(color = sample_type)) +  scale_color_cb_friendly()
+  geom_mark_ellipse(aes(color = .data[[column]])) +  scale_color_cb_friendly()
 ```
 
 ## Analysis of the variance by group
@@ -417,6 +418,7 @@ de_list=lapply(contrasts, function(contrast){
 ## MA plot {.tabset}
 
 This plot can help to:
+
 - Identify Differential Expression: Genes that show a significant log-fold change (M value away from 0) indicate changes in expression between conditions.
 - Assess Data Quality: The plot can help in identifying biases or systematic errors in the data. Ideally, most points should scatter around the M=0 line, indicating that there is no significant systematic difference between the conditions.
 - Visualize data dispersion: The distribution of points along the A-axis gives a sense of the spread of expression levels and any patterns or anomalies in the dataset.
@@ -537,7 +539,6 @@ for (contrast in names(de_list)){
 From the set of differentially expressed genes and using publicly available information about gene sets involved in biological processes and functions, we can calculate which biological processes and functions are significantly perturbed as a result of the treatment. 
 
 ```{r}
-all_in_life=get_databases()
 all_in_life=get_databases_v2()
 ```
 
@@ -571,7 +572,7 @@ fa_gsea_list=lapply(de_list,function(contrast){
 # multiple times
 dt_list=list()
 for (contrast in names(de_list)){
-  res_sig=fa_gsea_list[[contrast]]
+  res_sig=fa_gsea_list[[contrast]] %>% filter(padj < 0.05)
   dt_list=c(dt_list, 
             list(h3(contrast)), 
             list(sanitize_datatable(res_sig)))
@@ -622,7 +623,7 @@ fa_list=lapply(de_list,function(contrast){
 # multiple times
 dt_list=list()
 for (contrast in names(de_list)){
-  res_sig=fa_list[[contrast]][["all"]]
+  res_sig=fa_list[[contrast]][["all"]] %>% filter(padj < 0.05)
   dt_list=c(dt_list, 
             list(h3(contrast)), 
             list(sanitize_datatable(res_sig)))
@@ -636,7 +637,7 @@ tagList(dt_list)
 ```{r, results='asis'}
 dt_list=list()
 for (contrast in names(de_list)){
-  res_sig=fa_list[[contrast]][["down"]]
+  res_sig=fa_list[[contrast]][["down"]] %>% filter(padj < 0.05)
   dt_list=c(dt_list, 
             list(h3(contrast)), 
             list(sanitize_datatable(res_sig)))
@@ -650,7 +651,7 @@ tagList(dt_list)
 ```{r, results='asis'}
 dt_list=list()
 for (contrast in names(de_list)){
-  res_sig=fa_list[[contrast]][["up"]]
+  res_sig=fa_list[[contrast]][["up"]] %>% filter(padj < 0.05)
   dt_list=c(dt_list, 
             list(h3(contrast)), 
             list(sanitize_datatable(res_sig)))
@@ -668,18 +669,18 @@ if (!is.null(subset_value) & !is.null(subset_value)){
   filenames = "full"
 }
 for (contrast in names(contrasts)){
-  filenames = paste0(filenames, "_", contrast)
+  filename = paste0(filenames, "_", contrast)
   name_expression_fn=file.path(
     basedir,
-    str_interp("${filenames}_expression.csv"))
+    str_interp("${filename}_expression.csv"))
   
   name_deg_fn=file.path(
     basedir,
-    str_interp("${filenames}_deg.csv"))
+    str_interp("${filename}_deg.csv"))
   
   name_pathways_fn=file.path(
     basedir,
-    str_interp("${filenames}_pathways.csv"))
+    str_interp("${filename}_pathways.csv"))
 
   counts_norm=norm_matrix %>% as.data.frame() %>% 
     rownames_to_column("gene_id") %>% 

inst/templates/rnaseq/DE/GSVA.Rmd

@@ -36,7 +36,7 @@ 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/rnaseq/DE/Intersections.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(as.character(BiocManager::version()), "3.18")>=0)
 ```
 

inst/templates/rnaseq/QC/QC_nf-core.Rmd

@@ -36,7 +36,7 @@ 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/singlecell/Integration/norm_integration.rmd

@@ -30,7 +30,7 @@ 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)
 stopifnot(compareVersion(as.character(packageVersion("Seurat")), "5.0.0")>=0)
 ```
@@ -591,7 +591,7 @@ We take a look at how the clusters look at resolutions 0.1, 0.2,0.4, and 0.6
 ### 0.1
 
 ```{r umap_0.1}
-cluster_res <- 0.2
+cluster_res <- 0.1
 Idents(object = seurat_clust) <- paste0(prefix_clu, cluster_res)
 DimPlot(seurat_clust,
         reduction = show_this,

inst/templates/singlecell/QC/QC.rmd

@@ -16,7 +16,7 @@ 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)
 stopifnot(compareVersion(as.character(packageVersion("Seurat")), "5.0.0")>=0)
 ```

inst/templates/spatial/cosmx/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(BiocManager::version(), "3.18")>=0)
 stopifnot(compareVersion(package.version("Seurat"), "5.0.0")>=0)
 ```