From a29d73e4118382dab3e6d914c360cd7961ae58e7 Mon Sep 17 00:00:00 2001
From: Lorena Pantano <lorena.pantano@gmail.com>
Date: Thu, 18 Apr 2024 16:21:18 -0400
Subject: [PATCH] import-export accesory files

---
 DESCRIPTION                                    |  2 ++
 NAMESPACE                                      |  2 ++
 R/bcbioR-package.R                             |  7 +++++++
 R/hello.R                                      | 18 +++++++++++++++++-
 README.Rmd                                     |  2 ++
 README.md                                      |  3 +++
 .../templates/rnaseq/skeleton/README.md        |  6 +++++-
 .../rnaseq/skeleton/reports/DEG/run_markdown.R | 18 ++++++++++++++++++
 8 files changed, 56 insertions(+), 2 deletions(-)
 create mode 100644 R/bcbioR-package.R
 create mode 100644 inst/rmarkdown/templates/rnaseq/skeleton/reports/DEG/run_markdown.R

diff --git a/DESCRIPTION b/DESCRIPTION
index aec3cae..17cb675 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -10,3 +10,5 @@ LazyData: true
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
+Imports: 
+    stringr
diff --git a/NAMESPACE b/NAMESPACE
index 5a75104..193fed0 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,4 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(bcbio_gitignore)
 export(bcbio_set_project)
 export(bcbio_start_project)
+importFrom(stringr,str_replace_all)
diff --git a/R/bcbioR-package.R b/R/bcbioR-package.R
new file mode 100644
index 0000000..7fb162e
--- /dev/null
+++ b/R/bcbioR-package.R
@@ -0,0 +1,7 @@
+#' @keywords internal
+"_PACKAGE"
+
+## usethis namespace: start
+#' @importFrom stringr str_replace_all
+## usethis namespace: end
+NULL
diff --git a/R/hello.R b/R/hello.R
index e27efda..e148037 100644
--- a/R/hello.R
+++ b/R/hello.R
@@ -13,13 +13,23 @@
 #   Check Package:             'Cmd + Shift + E'
 #   Test Package:              'Cmd + Shift + T'
 
+.fix <- function(x){
+  x <- tolower(x) %>% str_replace_all(x, "[[:punct:]]", " ")
+  retunr(x)
+}
+
 #' @export
 bcbio_set_project <- function() {
   hbc_code <- readline("What is the hbc code:\n")
+  pi <- readline("What is PI last name:\n")
+  technology <- readline("What is the technology:\n")
+  tissue <- readline("What is the tissue:\n")
+  org <- readline("What is the organism:\n")
   project <- readline("What is the project name:\n")
   dropbox <- readline("What is the dropbox name:\n")
   github_org <- readline("What is the github organization:\n")
-  project_full <- paste0(project, "_", hbc_code)
+  #hbc_$technology_of_$pilastname_$intervention_on_$tissue_in_$organism_$hbccode
+  project_full <- paste(project, technology, fix(pi), project, tissue, organism, hbc_code, sep="_")
   github <- c(github_org,project_full)
   opts <- list(code=hbc_code, project=project_full,
                dropbox=file.path(dropbox,project_full),
@@ -33,6 +43,12 @@ bcbio_start_project <- function(options) {
 
 }
 
+#' @export
+bcbio_gitignore <- function(options) {
+
+}
+
+
 hello <- function() {
   print("Hello, world!")
 
diff --git a/README.Rmd b/README.Rmd
index 9192244..fbdc880 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -31,4 +31,6 @@ library(bcbioR)
 
 You'll still need to render `README.Rmd` regularly, to keep `README.md` up-to-date. `devtools::build_readme()` is handy for this.
 
+Use `usethis::use_import_from()` to make sure all the imports are correct.
+
 Don't forget to commit and push the resulting figure files, so they display on GitHub and CRAN.
diff --git a/README.md b/README.md
index 17d2f1e..ea6ea41 100644
--- a/README.md
+++ b/README.md
@@ -32,5 +32,8 @@ library(bcbioR)
 You’ll still need to render `README.Rmd` regularly, to keep `README.md`
 up-to-date. `devtools::build_readme()` is handy for this.
 
+Use `usethis::use_import_from()` to make sure all the imports are
+correct.
+
 Don’t forget to commit and push the resulting figure files, so they
 display on GitHub and CRAN.
diff --git a/inst/rmarkdown/templates/rnaseq/skeleton/README.md b/inst/rmarkdown/templates/rnaseq/skeleton/README.md
index 0e4c4ef..30016c5 100644
--- a/inst/rmarkdown/templates/rnaseq/skeleton/README.md
+++ b/inst/rmarkdown/templates/rnaseq/skeleton/README.md
@@ -3,7 +3,11 @@
 [ ] Replace Title in this file matching title projects
 [ ] run function`bcbio_set_project()` to set up information for this project
     - hbcxxxx code
+    - technology
+    - tissue
+    - organism
     - pi
-    - project name to be used in storage/github/dropbox
+    - project name
 [ ] run function `bcbio_set_git()` to set up git repository
 [ ] run function `bcbio_copy_dropbox()` to copy files to dropbox location
+
diff --git a/inst/rmarkdown/templates/rnaseq/skeleton/reports/DEG/run_markdown.R b/inst/rmarkdown/templates/rnaseq/skeleton/reports/DEG/run_markdown.R
new file mode 100644
index 0000000..4902560
--- /dev/null
+++ b/inst/rmarkdown/templates/rnaseq/skeleton/reports/DEG/run_markdown.R
@@ -0,0 +1,18 @@
+library(rmarkdown)
+
+render_de <- function(subset_value, numerator, denominator){
+  rmarkdown::render(input = "DEG.Rmd",
+                    output_dir = "reports",
+                    output_format = "html_document",
+                    output_file = paste0('DE_', subset_value, '_', numerator, '_vs_', denominator, '.html'),
+                    clean = TRUE,
+                    envir = new.env(),
+                    params = list(
+                      subset_value = subset_value,
+                      numerator = numerator,
+                      denominator = denominator
+                    )
+  )
+}
+
+render_de('HDFn', "TNF", "untreated")