Merge pull request #23 from NICHD-BSPC/devel

Merge 'devel' into 'main'

Author: mitraak

.Rbuildignore

@@ -10,3 +10,7 @@
 ^docs$
 ^pkgdown$
 ^\.github$
+^run-tests\.R$
+^application-map\.md$
+^carnation_application_note\.md$
+^testing*.md$

.github/workflows/conda.yml

@@ -10,7 +10,7 @@ name: conda
 
 on:
   push:
-    branches: [ "main" ]
+    branches: [ "main", "devel" ]
   pull_request:
     types:
       - opened
@@ -73,17 +73,25 @@ jobs:
           cd .. && mkdir tmp && cd tmp
 
           # build, check
-          R CMD build --no-manual ../carnation
-          R CMD check --no-manual --no-vignettes --timings --as-cran carnation_${VERSION}.tar.gz
+          time R CMD build --no-manual ../carnation
+          time R CMD check --no-manual --no-vignettes --timings --as-cran carnation_${VERSION}.tar.gz
 
           mv carnation_${VERSION}.tar.gz ${WORKDIR}/carnation.tar.gz
+          tar cvf rcmdcheck.tar.gz carnation.Rcheck
+          mv rcmdcheck.tar.gz ${WORKDIR}/rcmdcheck.tar.gz
 
       - name: env tarball
         uses: actions/upload-artifact@v4
         with:
           name: carnation-bundle
           path: carnation.tar.gz
 
+      - name: R CMD check log
+        uses: actions/upload-artifact@v4
+        with:
+          name: carnation-rcmdcheck
+          path: rcmdcheck.tar.gz
+
       - name: conda env pinned
         run: |
           source "${HOME}/conda/etc/profile.d/conda.sh"

.gitignore

@@ -1,2 +1,9 @@
+.DS_Store
 inst/doc
 docs
+debug*
+run_*.R
+test_*.R
+application*.md
+carnation_application_note.md
+testing*.md

DESCRIPTION

@@ -1,9 +1,13 @@
 Package: carnation
 Title: Shiny App to Explore RNA-Seq Analysis
-Version: 0.99.6
+Version: 0.99.7
 Authors@R:
-    person("Apratim", "Mitra", , "apratim.mitra@nih.gov", role = c("aut", "cre"),
-           comment = c(ORCID = "0000-0003-3279-0054"))
+    c(
+        person("Apratim", "Mitra", , "apratim.mitra@nih.gov",
+               role = c("aut", "cre"), comment = c(ORCID = "0000-0003-3279-0054")),
+        person("Ryan", "Dale", , "ryan.dale@nih.gov",
+               role = c("fnd"), comment = c(ORCID = "0000-0003-2664-3744"))
+    )
 Description: Interactive Shiny dashboard app that can be used to
     explore RNA-Seq analysis results including differential expression (DE),
     functional enrichment and pattern analysis. Several visualizations
@@ -17,9 +21,9 @@ Description: Interactive Shiny dashboard app that can be used to
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Depends:
-    R (>= 4.3.0)
+    R (>= 4.6.0)
 Imports:
     BiocParallel,
     colorspace,
@@ -57,10 +61,12 @@ Imports:
     yaml
 Suggests:
     airway,
+    BiocStyle,
     knitr,
     org.Hs.eg.db,
     DEGreport,
     rmarkdown,
+    testthat
 VignetteBuilder: knitr
 URL: https://nichd-bspc.github.io/carnation/
 BugReports: https://github.com/NICHD-BSPC/carnation/issues

NEWS.md

@@ -1,3 +1,25 @@
-# carnation 0.99.0
+# carnation
+
+## v0.99.7
+
+- Add unit tests
+- Address Bioconductor review comments
+
+## v0.99.6
+
+- Made `R CMD check` more efficient by switching multiple module server
+  examples to `examplesIf interactive()`.
+
+## v0.99.3
+
+- removed `clusterProfiler` & `DEGreport` from Suggests
+- added examples to exported functions
+
+## v0.99.1
+
+- Updated vignette with carnation app screenshots
+- Added vignette dependencies to Suggests
+
+## v0.99.0
 
 - carnation submitted to bioconductor for review

R/app.R

@@ -136,6 +136,7 @@ run_carnation <- function(credentials=NULL, passphrase=NULL, enable_admin=TRUE,
 
               icon = icon("sliders-h"), width = "400px",
               size='sm',
+              inputId="global_settings",
 
               tooltip = tooltipOptions(title = "Global settings")
 
@@ -316,6 +317,7 @@ run_carnation <- function(credentials=NULL, passphrase=NULL, enable_admin=TRUE,
 
               icon = icon("gear"), width = "400px",
               size='sm',
+              inputId="tab_settings",
 
               tooltip = tooltipOptions(title = "Settings")
 
@@ -400,6 +402,7 @@ run_carnation <- function(credentials=NULL, passphrase=NULL, enable_admin=TRUE,
 
               icon = icon("clipboard"), width = "400px",
               size='sm',
+              inputId="scratchpad",
 
               tooltip = tooltipOptions(title = "Gene scratchpad")
 
@@ -442,7 +445,9 @@ run_carnation <- function(credentials=NULL, passphrase=NULL, enable_admin=TRUE,
                 ) # conditionalPanel
               ), # column
               column(9, style='margin-top: 20px',
-                DTOutput('analysis_desc')
+                conditionalPanel('input.data_type == "Existing"',
+                  DTOutput('analysis_desc')
+                ) # conditionalPanel
               )
             ), # fluidRow
 

R/buttons.R

@@ -103,7 +103,7 @@ helpModal <- function(mdfile, title=NULL, ...){
 #' UI returns tagList with download button UI.
 #' Server invisibly returns NULL (used for side effects).
 #'
-#' @examples
+#' @examplesIf interactive()
 #' library(shiny)
 #' library(ggplot2)
 #'

R/carnation-pkg.R

@@ -0,0 +1,16 @@
+#' carnation
+#'
+#' `carnation` is an interactive Shiny dashboard that makes complex bulk RNA-Seq
+#' data more accessible and intuitive, integrating all facets of bulk RNA-Seq
+#' analysis using three modules - differential expression analysis, functional
+#' enrichment and pattern analysis.
+#'
+#' - Deeply explore analysis results from complex experiments using interactive plots.
+#' - Easily keep track of genes of interest using the 'Gene scratchpad'.
+#' - Use fuzzy search to filter and search functional enrichment results.
+#' - Visualize complex patterns using highly customizable gene plot.
+#' - Manage local data in single-user mode or deploy on a server to share with
+#'   collaborators using in-built user management system.
+#'
+#' @keywords internal
+'_PACKAGE'