merge magic

.gitignore

@@ -13,3 +13,9 @@ docs
 /doc/
 /Meta/
 .DS*
+inst/rmarkdown/templates/rnaseq/skeleton/DE/Multiplicative_DGE_Analysis.Rmd
+tests/*
+.Rdata
+.httr-oauth
+.DS_Store
+.quarto

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: 0.2.0
 Authors@R: person("Pantano", "Lorena", , "[email protected]",
             role = c("aut", "cre"))
 Description: Collaborative code repository at the Harvard Chan Bioinformatics Core.
@@ -20,8 +20,13 @@ Imports:
     grDevices,
     R.utils,
     readr,
-    fs,
     withr
+    usethis,
+    fs,
+    jsonlite,
+    yaml,
+    whisker,
+    rlang
 Suggests: 
     knitr,
     rmarkdown,

NAMESPACE

@@ -8,11 +8,14 @@ export(cb_friendly_pal)
 export(list_cb_friendly_cols)
 export(scale_color_cb_friendly)
 export(scale_fill_cb_friendly)
+export(use_bcbio_projects)
 import(DESeq2)
 import(R.utils)
+import(fs)
 import(ggplot2)
 import(ggprism)
 import(hues)
+import(usethis)
 importFrom(grDevices,colorRampPalette)
 importFrom(magrittr,"%>%")
 importFrom(readr,read_csv)

R/app.R

@@ -0,0 +1,51 @@
+# Global variables can go here
+library(stringr)
+.fix <- function(x){
+  x <- tolower(x)
+  x <- str_replace_all(x, "[[:punct:]]", "_")
+  x <- str_replace_all(x, " ", "_")
+  return(x)
+}
+
+
+# Define the UI
+ui <- fluidPage(
+  # Application title
+  titlePanel("Create project name"),
+
+  sidebarLayout(
+    # Sidebar with a slider and selection inputs
+    sidebarPanel(
+      textInput('hbc', 'hbc-code (no letters)', value = "00000"),
+      textInput('pi', 'What is PI last name:', value = "lastname"),
+      textInput('scientist', 'What is the scientist last name:', value = "scientist"),
+      textInput('tech', 'What is the technology:', value = "rnaseq"),
+      textInput('tissue', 'What is the tissue:', value = "mix|cells|heart"),
+      textInput('org', 'What is the organism:', value = "mix|human"),
+      textInput('proj', 'What is the project name:', value = "this_analysis_is_cool"),
+
+    ),
+
+    # Show Word Cloud
+    mainPanel(
+      br("Suggested project name:"),
+      br(),
+      verbatimTextOutput('project')
+    )
+  )
+)
+
+
+# Define the server code
+server <- function(input, output, session) {
+  output$project <- renderText({
+    hbc_code <- paste0("hbc", input$hbc)
+    project_full <- paste(input$tech, .fix(input$pi), .fix(input$scientist),
+                          .fix(input$proj),
+                          input$tissue, input$org, hbc_code, sep="_")
+    project_full
+  })
+}
+
+# Return a Shiny app object
+shinyApp(ui = ui, server = server)

R/bcbioR-package.R

@@ -9,6 +9,8 @@
 ## usethis namespace: end
 #' @import DESeq2
 #' @import ggplot2
+#' @import usethis
+#' @import fs
 #' @import hues
 #' @import ggprism
 #' @import R.utils