Nothing
###make reactive database given reference genome
txdb= reactive({if (input$UCSC_Genome == "hg19"){
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene}
else{
txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene}
})
#################make reactive dataframe given input file
mydata <- reactiveVal()
observeEvent(input$file1, {
tmp <- read.table(input$file1$datapath,
header = input$header, stringsAsFactors = FALSE)
colnames(tmp)[1:3]=c("chromosome","start","end")
n= length(colnames(tmp)[-1:-3])
a=rep(head(seq_along(tmp),-3), each=2)
colnames(tmp)[-1:-3]=paste0(c("sample_","nucleotide_"), a[1:n])
## do whatever is needed to parse the data
mydata(tmp)
})
observeEvent(input$pileup, {
tmp_pileup <- pileup_input()
colnames(tmp_pileup)[1:3]=c("chromosome","start","end")
n= length(colnames(tmp_pileup)[-1:-3])
a=rep(head(seq_along(tmp_pileup),-3), each=2)
colnames(tmp_pileup)[-1:-3]=paste0(c("sample_","nucleotide_"), a[1:n])
## do whatever is needed to parse the data
mydata(tmp_pileup)
})
#example.file <- system.file(
# "extdata",
#"POLG.example.bed",
#package = "uncoverappLib"
#)
#observeEvent(input$example_data, {
# polg= read.table(example.file)
#colnames(polg)= c("chromosome","start","end","sample_1","nucleotide_1" )
#mydata(polg)
#})
###Output of loaded file
###make reactive dataset given input choosed by users
mysample<-reactive({
if (is.null(mydata()))
return(NULL)
#i= input$Sample
num= input$Sample
i=paste0("sample_",num)
nucleodites= paste0("nucleotide_",num)
#print(mydata())
mydata() %>%
dplyr:: select(chromosome, start, end,i,nucleodites) %>%
dplyr::rename(coverage=i) %>%
dplyr::rename(counts= nucleodites)
})
filtered_low<- reactive ({
if (is.null(mysample()))
return(NULL)
mysample() %>%
dplyr::select(-c(counts)) %>%
dplyr::filter(chromosome == Chromosome(),
coverage <= as.numeric(input$coverage_co))
})
filtered_high<- reactive ({
if (is.null(mysample()))
return(NULL)
mysample() %>%
dplyr::select(-c(counts)) %>%
dplyr::filter(chromosome == Chromosome(),
coverage > as.numeric(input$coverage_co))
})
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