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JSON_UROPA/JASON_UROPA_queries_V8.R
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#================================ | |
# | |
# Initialization | |
# | |
#================================ | |
# Loading in libraries | |
library(shiny) | |
library(shinydashboard) | |
library(shinyBS) | |
# Defining the parameters | |
startpoint <- 1 | |
# User-defined functions | |
JU_resformat <- function (var1, var2, var3, var4, var5, var6, var7, var8, distance_up, distance_down) { | |
var3_read <- gsub("[[:space:]]", "", unlist(strsplit(var3, ";"))) | |
if (length (var3_read) <= 1) { | |
concatline <- paste("{","\"feature\"",":\"", var1,"\", ", | |
"\"feature.anchor\"",":\"", var2,"\", ", | |
"\"show.attribute\":\"", var3,"\", ", | |
"\"internals\"",":\"", var4,"\", ", | |
"\"attribute.value\"",":\"", var5,"\", ", | |
"\"strand\"",":\"",var6,"\", ", | |
"\"attribute.value\"",":\"", var7,"\", ", | |
"\"direction\"",":\"", var8,"\", ", | |
"\"distance\"",":","[",distance_up,", ",distance_down,"]","}", sep = "" | |
) | |
} else { | |
var3_conc <- paste ("[\"", var3_read[1], "\"", sep = "") | |
for (i in 2:length(var3_read)) { | |
var3_i <- var3_read[i] | |
var3_conc <- paste (var3_conc, paste (", \"", var3_i, "\"", sep = "")) | |
} | |
var3_conc <- paste (var3_conc, "]", sep = "") | |
concatline <- paste("{","\"feature\"",":\"", var1,"\", ", | |
"\"feature.anchor\"",":\"", var2,"\", ", | |
"\"show.attribute\":", var3_conc,", ", | |
"\"internals\"",":\"", var4,"\", ", | |
"\"filter.attribute\"",":\"", var5,"\", ", | |
"\"attribute.value\"",":\"", var6,"\", ", | |
"\"strand\"",":\"",var7,"\", ", | |
"\"direction\"",":\"", var8,"\", ", | |
"\"distance\"",":","[",distance_up,", ",distance_down,"]","}", sep = "" | |
) | |
} | |
return (concatline) | |
} | |
# Creating modules | |
# First module | |
#-------------------------------- | |
# A module to read the inputs | |
# UI-part | |
PrintTablesUI <- function(id, label = "ui1UI") { | |
ns <- NS(id) | |
shinyUI( | |
fluidRow( | |
box(background = "light-blue",title= "query...",width=2), | |
box(background = "light-blue",title= "JASON_UROPA_queries", | |
column(width = 6, | |
textInput("var1","feature"), | |
textInput("var6","attribute.value"), | |
textInput("var5","filter.attribute"), | |
textInput("var3","show.attribute"), | |
# bsTooltip("var3", "type attributes between quotation marks separated with comma", | |
# "right", options = list(container = "body")), | |
sliderInput("distance_up", "distance_uptream", min = -10000, max = 10000, value = c(500))) | |
, | |
column(width = 6, | |
selectInput("var7","strand",choices=c("+","-","both")), | |
selectInput("var2","feature.anchor",choices=c("start","center","end")), | |
selectInput("var4","internals",choices=c("none","center","any")), | |
selectInput("var8","direction",choices=c("any_direction","upstream","downstream")), | |
sliderInput("distance_down", "distance_upstream",min = -10000, max = 10000, value = c(500) | |
) ) | |
) | |
) | |
) | |
} | |
# Server-part | |
PrintTables <- function(input, output, session) { | |
strinputvars <- list( | |
var1_ret <- reactive({input$var1}), | |
var2_ret <- reactive({input$var2}), | |
var2_ret <- reactive({input$var3}), | |
var2_ret <- reactive({input$var4}), | |
var2_ret <- reactive({input$var5}), | |
var2_ret <- reactive({input$var6}), | |
var2_ret <- reactive({input$var7}), | |
var2_ret <- reactive({input$var8}), | |
distanceUp_ret <- reactive({input$distance_up}), | |
distanceDown_ret <- reactive({input$distance_down}) | |
) | |
return(strinputvars) | |
} | |
#================================ | |
# | |
# Program code | |
# | |
#================================ | |
# We'll save it in a variable `ui` so that we can preview it in the console | |
ui <- dashboardPage( | |
dashboardHeader(title=div(img(src="site.logo.jpg"),"JASON_UROPA_queries")), | |
dashboardSidebar( | |
fluidRow( | |
column(width=12, | |
selectInput("species_GTF","select species",choices=c("mus musculus","homo sapiens")), | |
radioButtons("gtf_files" ,"Select gtf file", | |
c("gencode.v22.genes.gtf"="human","gencode.vM5.genes.gtf"="mouse","other"="other")), | |
uiOutput("textORdate"), | |
#fileInput("gtf files","Upload gtf file (tab-separated)"), | |
fileInput("file1", "Upload bed File")), | |
column(width=12, | |
selectInput("priority"," prioritized query",choices=c("FALSE","TRUE"))), | |
column(width = 12, | |
numericInput("NrQuery","Enter number of queries", 2, min=1, max=NaN), | |
actionButton("addqueries", "Add Module"), | |
actionButton("printres", "Save query")) | |
)), dashboardBody( | |
div(id = "ui_zero"), | |
div(id = "ui_zero2") | |
) | |
) | |
server <- (function(input, output, session) { | |
output$textORdate <- renderUI({ | |
#validate( | |
# need(!is.null(input$gtffiles), "please select a input type") | |
# ) | |
if(input$gtf_files =="other"){ | |
fileInput("file2","Upload gtf file (tab-separated)") | |
}else{ | |
} | |
}) | |
# Print the tables (first module) | |
observeEvent(input$addqueries, { | |
for (counter in startpoint:input$NrQuery) { | |
ID <- paste0("c", counter) | |
insertUI("#ui_zero", "beforeEnd", PrintTablesUI(ID)) | |
module_iterres <- callModule(PrintTables, ID) | |
assign (paste("var_", ID, sep = ""), value = module_iterres, pos = 1) | |
observeEvent(input$printres, { | |
outputID <- "example" | |
insertUI("#ui_zero2", "beforeEnd", uiOutput(outputID)) | |
uiOutput(outputID) | |
resline <- paste("\"", "queries", "\"", ":[", sep = "") | |
output$example <- renderUI({ | |
for (counter in startpoint:input$NrQuery) { | |
ID <- paste0("c", counter) | |
fieldname <- eval(parse(text = paste("var_", ID, sep = ""))) | |
if (counter == startpoint) { | |
resline <- paste (resline, JU_resformat(fieldname[[1]](), fieldname[[2]](), fieldname[[3]](), fieldname[[4]](), fieldname[[5]](), fieldname[[6]](), fieldname[[7]](), fieldname[[8]](), fieldname[[9]](), fieldname[[10]]()), sep = "") | |
} else { | |
resline <- paste (resline, ",\n", JU_resformat(fieldname[[1]](), fieldname[[2]](), fieldname[[3]](), fieldname[[4]](), fieldname[[5]](), fieldname[[6]](), fieldname[[7]](), fieldname[[8]](), fieldname[[9]](), fieldname[[10]]()), sep = "") | |
} | |
} | |
resline <- paste (resline, "]", | |
",\n\"priority\": \"", input$priority, "\",\n", | |
"\"gtf\": \"", input$file2$name, "\",\n", | |
"\"bed\": \"", input$file1$name, "\"", sep = "") | |
write.table (resline, "configuration.txt", quote = F, col.names = F, row.names = F) | |
}) | |
}) | |
} | |
}) | |
}) | |
# Running the program | |
shinyApp(ui = ui, server = server) | |