V0.99.9

.github/workflows/conda.yml

@@ -106,7 +106,7 @@ jobs:
           source "${HOME}/conda/etc/profile.d/conda.sh"
           conda activate ../env
 
-          Rscript -e "setRepositories(ind=1:5); remotes::install_github('NICHD-BSPC/carnation', upgrade='never')"
+          Rscript -e "setRepositories(ind=1:5); remotes::install_github('NICHD-BSPC/carnation@r4.3', upgrade='never')"
           Rscript -e "library(carnation)"
 
 

.github/workflows/pkgdown.yaml

@@ -61,7 +61,7 @@ jobs:
           source "${HOME}/conda/etc/profile.d/conda.sh"
           conda activate ../env
 
-          Rscript -e "setRepositories(ind=1:5); remotes::install_github('NICHD-BSPC/carnation', upgrade='never')"
+          Rscript -e "setRepositories(ind=1:5); remotes::install_github('NICHD-BSPC/carnation@r4.3', upgrade='never')"
           Rscript -e "pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)"
 
       - name: Deploy to GitHub pages 🚀

DESCRIPTION

@@ -1,23 +1,27 @@
 Package: carnation
-Title: Shiny App to Explore RNA-Seq Analysis
-Version: 0.99.8
+Title: Interactive Exploration & Management of RNA-Seq Analyses
+Version: 0.99.9
 Authors@R:
     c(
         person("Apratim", "Mitra", , "apratim.mitra@nih.gov",
                role = c("aut", "cre"), comment = c(ORCID = "0000-0003-3279-0054")),
+        person(c("Matthew", "Tyler"), "Menold", , "matthew.menold@gmail.com",
+               role = c("ctb"), comment = c(ORCID = "0009-0007-4728-2470")),
         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),
+Description: This package provides a highly interactive & modular shiny app to
+    explore three facets of RNA-Seq analysis: differential expression (DE),
     functional enrichment and pattern analysis. Several visualizations
     are implemented to provide a wide-ranging view of data sets. For
     DE analysis, we provide PCA plot, MA plot, Upset plot & heatmaps,
     in addition to a highly customizable gene plot.  Seven different
     visualizations are available for functional enrichment analysis,
-    and we also support gene pattern analysis. In addition, the app
-    provides a platform to manage multiple projects and user groups
-    that can be run on a central server.
+    and we also support gene pattern analysis. Genes of interest can
+    be tracked across all modules using the gene scratchpad. In addition,
+    carnation provides an integrated platform to manage multiple projects
+    and user access that can be run on a central server to share with
+    collaborators.
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -43,6 +43,7 @@ export(horizonUI)
 export(in_admin_group)
 export(install_carnation)
 export(is_site_admin)
+export(is_valid_pattern_obj)
 export(loadDataServer)
 export(loadDataUI)
 export(maPlotServer)
@@ -155,13 +156,17 @@ importFrom(htmltools,tags)
 importFrom(htmltools,withTags)
 importFrom(igraph,"V<-")
 importFrom(igraph,V)
+importFrom(methods,.hasSlot)
 importFrom(methods,new)
 importFrom(plotly,add_markers)
 importFrom(plotly,add_trace)
+importFrom(plotly,event_data)
+importFrom(plotly,event_register)
 importFrom(plotly,ggplotly)
 importFrom(plotly,layout)
 importFrom(plotly,plot_ly)
 importFrom(plotly,plotlyOutput)
+importFrom(plotly,plotlyProxy)
 importFrom(plotly,renderPlotly)
 importFrom(plotly,save_image)
 importFrom(plotly,toWebGL)

NEWS.md

@@ -1,5 +1,18 @@
 # carnation
 
+## v0.99.9
+
+- carnation now supports `edgeR` and `limma` output in differential
+  expression analysis.
+- The scatter plot now allows gene selection directly from the plot
+  and viewed in the table. Genes selected in the table can be added
+  to the gene scratchpad and tracked across the app.
+- The main loading page now shows the currently loaded dataset.
+  This prevents accidentally reloading or replacing the current
+  data.
+- Pattern analysis can now be added to a carnation object via
+  the `Load data` module, either in TSV or Rds format.
+
 ## v0.99.8
 
 - Add packages to `Suggests::` to address build issues.

R/app.R

@@ -453,7 +453,12 @@ run_carnation <- function(credentials=NULL, passphrase=NULL, enable_admin=TRUE,
 
             withSpinner(
               uiOutput('load_ui')
-            ) # withSpinner
+            ),  # withSpinner
+
+            br(),
+            fluidRow(
+              column(3, uiOutput('current_obj'))
+            ) # fluidRow
           ), # tabPanel
 
           tabPanel('DE analysis',
@@ -647,6 +652,9 @@ run_carnation <- function(credentials=NULL, passphrase=NULL, enable_admin=TRUE,
     # list to hold original object and file path
     original <- reactiveValues(obj=NULL, path=NULL)
 
+    # reactiveValues to hold loaded project
+    current <- reactiveValues(proj=NULL, analysis=NULL)
+
     # list to hold user details
     user_details <- reactiveValues(username=NULL, admin=FALSE)
 
@@ -1073,6 +1081,46 @@ run_carnation <- function(credentials=NULL, passphrase=NULL, enable_admin=TRUE,
                                x
                            })
 
+      # make sure 'padj' & 'log2FoldChange' columns exist in res objects
+      # or supported alternatives exist
+      sanitized_res_list <- obj[[ res.name ]]
+
+      # supported column names
+      column_names <- config()$server$de_analysis$column_names
+      defaults <- names(column_names)
+
+      # these res objects will be dropped
+      drop_res_names <- NULL
+
+      for(name in names(sanitized_res_list)){
+        res <- sanitized_res_list[[ name ]]$res
+        res <- as.data.frame(res)
+
+        for(cname in defaults){
+          idx <- colnames(res) %in% column_names[[ cname ]]
+
+          # if matches exist
+          if(sum(idx) > 0){
+            if(sum(idx) > 1){
+            # only use the first match if multiple matches
+            # and show warning
+              message('Warning: Ambiguous ', cname, 'column for ', name, '.\nUsing ', colnames(res)[which(idx)[1]])
+            }
+
+            idx <- which(idx)[1]
+            colnames(res)[idx] <- cname
+          } else {
+            message('Unsupported res type for ', name, ':', cname, ' column not found, skipping')
+            drop_res_names <- c(drop_res_names, name)
+          }
+        }
+        sanitized_res_list[[ name ]]$res <- res
+      }
+
+      # remove unsupported res objects
+      sanitized_res_list <- sanitized_res_list[ !names(sanitized_res_list) %in% drop_res_names ]
+      obj[[ res.name ]] <- sanitized_res_list
+
       # add obj slots to reactive values
       obj <- make_final_object(obj)
 
@@ -1237,8 +1285,28 @@ run_carnation <- function(credentials=NULL, passphrase=NULL, enable_admin=TRUE,
                         selected='DE analysis')
       updateTabsetPanel(session, inputId='de_mode',
                         selected='Summary')
+
+      # update current project
+      current$proj <- input$dds
+
+      al <- assay.list$l[[ input$dds ]]
+      idx <- which(unname(al) == input$assay)
+      current$analysis <- names(assay.list$l[[ input$dds ]])[idx]
+
     }) # observeEvent load data
 
+    # show loaded dataset
+    output$current_obj <- renderUI({
+      req(current$proj)
+
+      tags$div(
+        class='div-stats-card',
+        tags$p('Currently loaded:'),
+        tags$p('  - Project: ', tags$i(current$proj)),
+        tags$p('  - Analysis: ', tags$i(current$analysis))
+      )
+    })
+
     # update comparison menus after load
     observeEvent(app_object$res, {
       validate(
@@ -1604,7 +1672,25 @@ run_carnation <- function(credentials=NULL, passphrase=NULL, enable_admin=TRUE,
            gene.to.plot=gene_scratchpad())
     })
 
-    scatterPlotServer('scatterplot', app_object, scatterplot_args, config)
+    scatter_data <- scatterPlotServer('scatterplot',
+                                      app_object,
+                                      scatterplot_args,
+                                      gene_scratchpad,
+                                      reactive({ input$reset.genes }),
+                                      config)
+
+    observeEvent(scatter_data(), {
+      g <- scatter_data()$genes
+
+      # only update scratchpad if different genes returned
+      if(length(setdiff(g, input$gene.to.plot)) != 0){
+        # update gene selector with clicked genes
+        updateSelectizeInput(session, 'gene.to.plot',
+                             choices=gene.id$gene,
+                             selected=g,
+                             server=TRUE)
+      }
+    })
 
     ##################### UpSet plot #########################
 

R/carnation-pkg.R

@@ -12,5 +12,7 @@
 #' - Manage local data in single-user mode or deploy on a server to share with
 #'   collaborators using in-built user management system.
 #'
+#' Main function to run the app: [run_carnation()]
+#'
 #' @keywords internal
 '_PACKAGE'