Merge branch 'vizapp_demo' into 'master'

addes sample chipseq charts for vizapp

See merge request !4

astrocyte_pkg.yml

@@ -142,7 +142,8 @@ vizapp_cran_packages:
 # List of any Bioconductor packages, not provided by the modules, that must be made
 # available to the vizapp
 vizapp_bioc_packages:
-  -
+  - ChIPseeker
+  - org.Hs.eg.db
 
 # List of any packages to install from GitHub using devtools, that must be
 # made availavle to the vizapp

vizapp/server.R

@@ -3,18 +3,43 @@
 library(shiny)
 library(shinyFiles)
 
+library(ChIPseeker)
+library(TxDb.Hsapiens.UCSC.hg19.knownGene)
+
 # Results are available in the directory specified by the outputDir environment
 # variable, red by Sys.getenv
 
 rootdir <- Sys.getenv('outputDir')
 
-
 shinyServer(function(input, output, session) {
 
     # The backend for a simple file chooser, restricted to the
     # rootdir we obtained above.
     # See https://github.com/thomasp85/shinyFiles
 
-    shinyFileChoose(input, 'files', roots=c('workflow'=rootdir), filetypes=c('', 'bed', 'xls','wig'), session=session)
 
+  observe({
+      print(getwd());
+      files <- list.files(path = rootdir, pattern = ".bed")
+      cat("\nBed files found:\n\n")
+     
+      filenames <- as.list(paste0(rootdir, files));
+      names(filenames) <- files;
+      print(filenames)
+      
+      txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
+      
+      
+      peakAnnoList <- lapply(filenames, annotatePeak, TxDb=txdb,
+                             tssRegion=c(-3000, 3000), verbose=FALSE)
+      
+      output$plot1 <- renderPlot({
+        
+        plotAnnoBar(peakAnnoList)
+      })
+      output$plot2 <- renderPlot({
+        
+        plotDistToTSS(peakAnnoList)
+      })
+  })
 })

vizapp/ui.R

@@ -7,24 +7,9 @@ shinyUI(fluidPage(
   verticalLayout(
 
     # Application title
-    titlePanel("Astrocyte Example"),
+    titlePanel("Astrocyte ChiPseq Example"),
 
-    wellPanel(
-
-        helpText("This is a minimal example, demonstrating how
-        a Shiny visualization application can access the output of a workflow.
-        Here we provide a file browser using the shinyFiles package. Real
-        Astrocyte vizapps would provide custom methods to access and visualize
-        output."),
-
-        helpText("The workflow output is in the directory set in the
-        outputDir environment variable. this can be retrieved in R with the
-        command Sys.getenv('outputDir')"),
-
-        # A simple file browser within the workflow output directory
-        # See https://github.com/thomasp85/shinyFiles
-        shinyFilesButton('files', label='Browse workflow output', title='Please select a file', multiple=FALSE)
-
-    )
+    plotOutput("plot1"),
+    plotOutput("plot2")
   )
 ))
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