/usr/lib/R/site-library/ensembldb/shinyHappyPeople/server.R is in r-bioc-ensembldb 2.2.2-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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packs <- installed.packages()
epacks <- packs[grep(packs, pattern="^Ens")]
## library(EnsDb.Hsapiens.v75)
## edb <- EnsDb.Hsapiens.v75
TheFilter <- function(input){
Cond <- input$condition
## check if we've got something to split...
Vals <- input$geneName
## check if we've got ,
if(length(grep(Vals, pattern=",")) > 0){
## don't want whitespaces here...
Vals <- gsub(Vals, pattern=" ", replacement="", fixed=TRUE)
Vals <- unlist(strsplit(Vals, split=","))
}
if(length(grep(Vals, pattern=" ", fixed=TRUE)) > 0){
Vals <- unlist(strsplit(Vals, split=" ", fixed=TRUE))
}
if(input$type=="Gene name"){
return(GenenameFilter(Vals, condition=Cond))
}
if(input$type=="Chrom name"){
return(SeqNameFilter(Vals, condition=Cond))
}
if(input$type=="Gene biotype"){
return(GeneBiotypeFilter(Vals, condition=Cond))
}
if(input$type=="Tx biotype"){
return(TxBiotypeFilter(Vals, condition=Cond))
}
}
## checkSelectedPackage <- function(input){
## if(is.null(input$package)){
## return(FALSE)
## }else{
## require(input$package, character.only=TRUE)
## message("Assigning ", input$package, " to variable edb.")
## assign("edb", get(input$package), envir=globalenv())
## return(TRUE)
## }
## }
## Based on the given EnsDb package name it loads the library and returns
## the object.
getEdb <- function(x){
require(x, character.only=TRUE)
return(get(x))
}
## Define server logic required to draw a histogram
shinyServer(function(input, output) {
## Generate the select field for the package...
output$packages <- renderUI(
selectInput("package", "Select installed EnsDb package", as.list(epacks))
)
selectedPackage <- reactive({
names(epacks) <- epacks
## epacks <- sapply(epacks, as.symbol)
## load the package.
if(length(input$package) > 0){
require(input$package, character.only=TRUE)
## Actually, should be enough to just return input$package...
##return(switch(input$package, epacks))
return(getEdb(input$package))
}else{
return(NULL)
}
})
## Metadata infos
output$metadata_organism <- renderText({
edb <- selectedPackage()
if(!is.null(edb)){
## db <- getEdb(edb)
paste0("Organism: ", organism(edb))
}
})
output$metadata_ensembl <- renderText({
edb <- selectedPackage()
if(!is.null(edb)){
## db <- getEdb(edb)
md <- metadata(edb)
rownames(md) <- md$name
paste0("Ensembl version: ", md["ensembl_version", "value"])
}
})
output$metadata_genome <- renderText({
edb <- selectedPackage()
if(!is.null(edb)){
## db <- getEdb(edb)
md <- metadata(edb)
rownames(md) <- md$name
paste0("Genome build: ", md["genome_build", "value"])
}
})
output$genename <- renderText({
if(length(input$geneName) > 0){
input$geneName
}else{
return()
}
})
## That's the actual queries for genes, transcripts and exons...
output$Genes <- renderDataTable({
## if(!checkSelectedPackage(input))
## return()
if(length(input$package) == 0)
return(NULL)
if(!is.na(input$geneName) & length(input$geneName) > 0 & input$geneName!=""){
edb <- selectedPackage()
res <- genes(edb, filter=TheFilter(input),
return.type="data.frame")
assign(".ENS_TMP_RES", res, envir=globalenv())
return(res)
}
})
output$Transcripts <- renderDataTable({
if(length(input$package) == 0)
return(NULL)
if(!is.na(input$geneName) & length(input$geneName) > 0 & input$geneName!=""){
edb <- selectedPackage()
res <- transcripts(edb, filter=TheFilter(input),
return.type="data.frame")
assign(".ENS_TMP_RES", res, envir=globalenv())
return(res)
}
})
output$Exons <- renderDataTable({
if(length(input$package) == 0)
return(NULL)
if(!is.na(input$geneName) & length(input$geneName) > 0 & input$geneName!=""){
edb <- selectedPackage()
res <- exons(edb, filter=TheFilter(input),
return.type="data.frame")
assign(".ENS_TMP_RES", res, envir=globalenv())
return(res)
}
})
observe({
if(input$closeButton > 0){
## OK, now, gather all the data and return it in the selected format.
edb <- selectedPackage()
resType <- input$returnType
resTab <- input$resultTab
res <- NULL
## If result type is data.frame we just return what we've got.
if(resType == "data.frame"){
res <- get(".ENS_TMP_RES")
}else{
## Otherwise we have to fetch a little bit more data, thus, we perform the
## query again and return it as GRanges.
if(resTab == "Genes")
res <- genes(edb, filter=TheFilter(input), return.type="GRanges")
if(resTab == "Transcripts")
res <- transcripts(edb,filter=TheFilter(input), return.type="GRanges")
if(resTab == "Exons")
res <- exons(edb,filter=TheFilter(input), return.type="GRanges")
}
rm(".ENS_TMP_RES", envir=globalenv())
stopApp(res)
}
})
})
## ## Define server logic required to draw a histogram
## shinyServer(function(input, output) {
## ## generate the select field for the package...
## output$packages <- renderUI(
## selectInput("package", "Select EnsDb package", as.list(epacks))
## )
## ## generating metadata info.
## output$metadata_organism <- renderText({
## if(!checkSelectedPackage(input))
## return()
## paste0("Organism: ", organism(edb))
## })
## output$metadata_ensembl <- renderText({
## if(!checkSelectedPackage(input))
## return()
## md <- metadata(edb)
## rownames(md) <- md$name
## paste0("Ensembl version: ", md["ensembl_version", "value"])
## })
## output$metadata_genome <- renderText({
## if(!checkSelectedPackage(input))
## return()
## md <- metadata(edb)
## rownames(md) <- md$name
## paste0("Genome build: ", md["genome_build", "value"])
## })
## ## output$genename <- renderText({
## ## if(!checkSelectedPackage(input))
## ## return()
## ## input$geneName
## ## })
## ## That's the actual queries for genes, transcripts and exons...
## output$Genes <- renderDataTable({
## if(!checkSelectedPackage(input))
## return()
## if(!is.na(input$geneName) & length(input$geneName) > 0 & input$geneName!=""){
## res <- genes(edb, filter=TheFilter(input),
## return.type="data.frame")
## return(res)
## }
## })
## output$Transcripts <- renderDataTable({
## if(!checkSelectedPackage(input))
## return()
## if(!is.na(input$geneName) & length(input$geneName) > 0 & input$geneName!=""){
## res <- transcripts(edb, filter=TheFilter(input),
## return.type="data.frame")
## return(res)
## }
## })
## output$Exons <- renderDataTable({
## if(!checkSelectedPackage(input))
## return()
## if(!is.na(input$geneName) & length(input$geneName) > 0 & input$geneName!=""){
## res <- exons(edb, filter=TheFilter(input),
## return.type="data.frame")
## return(res)
## }
## })
## ## observe({
## ## if(input$Close > 0){
## ## stopApp("AAARGHHH")
## ## }
## ## })
## })
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