Commit d149c613 authored by Peng Lian's avatar Peng Lian
Browse files

Merge branch 'vizapp_demo' into 'master'

addes sample chipseq charts for vizapp

See merge request !4
parents 17038dcb eafd41dd
......@@ -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
......
......@@ -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)
})
})
})
......@@ -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")
)
))
\ No newline at end of file
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