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Now with progress bar(5 minutes)
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#================================ | ||
# | ||
# Initialization | ||
# | ||
#================================ | ||
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# Loading in libraries | ||
library(shiny) | ||
library(shinydashboard) | ||
library(shinyBS) | ||
library(data.table) | ||
library(readr) | ||
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##### define popover for radiobuttons in the sidebar | ||
radioTooltip <- function(id, choice, title, placement = "bottom", trigger = "hover", options = NULL){ | ||
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options = shinyBS:::buildTooltipOrPopoverOptionsList(title, placement, trigger, options) | ||
options = paste0("{'", paste(names(options), options, sep = "': '", collapse = "', '"), "'}") | ||
bsTag <- shiny::tags$script(shiny::HTML(paste0(" | ||
$(document).ready(function() { | ||
setTimeout(function() { | ||
$('input', $('#", id, "')).each(function(){ | ||
if(this.getAttribute('value') == '", choice, "') { | ||
opts = $.extend(", options, ", {html: true}); | ||
$(this.parentElement).tooltip('destroy'); | ||
$(this.parentElement).tooltip(opts); | ||
} | ||
}) | ||
}, 500) | ||
}); | ||
"))) | ||
htmltools::attachDependencies(bsTag, shinyBS:::shinyBSDep) | ||
} | ||
########### end of define popover for radiobuttons in the sidebar | ||
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# Defining the parameters | ||
startpoint <- 1 | ||
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# User-defined functions | ||
fileInput2 <- function(inputId, label = NULL, labelIcon = NULL, multiple = FALSE, | ||
accept = NULL, width = NULL, progress = TRUE, ...) { | ||
# add class fileinput_2 defined in UI to hide the inputTag | ||
inputTag <- tags$input(id = inputId, name = inputId, type = "file", | ||
class = "fileinput_2") | ||
if (multiple) | ||
inputTag$attribs$multiple <- "multiple" | ||
if (length(accept) > 0) | ||
inputTag$attribs$accept <- paste(accept, collapse = ",") | ||
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div(..., style = if (!is.null(width)) paste0("width: ", validateCssUnit(width), ";"), | ||
inputTag, | ||
# label customized with an action button | ||
tags$label(`for` = inputId, div(icon(labelIcon), label, | ||
class = "btn btn-default action-button")), | ||
# optionally display a progress bar | ||
if(progress) | ||
tags$div(id = paste(inputId, "_progress", sep = ""), | ||
class = "progress shiny-file-input-progress", | ||
tags$div(class = "progress-bar") | ||
) | ||
) | ||
} | ||
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# A print function to create the configuration file format | ||
JU_resformat <- function (var1, var2, var3, var4, var5, var6, var7, var8, distance_up, distance_down) { | ||
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strprintline <- "{" | ||
# var1 | ||
if (!is.null(var1)) { | ||
if (length(var1) == 1) { | ||
strprintline <- paste (strprintline, "\"feature\"",":\"", var1,"\", ", sep = "") | ||
} else { | ||
var1_conc <- paste ("[\"", var1[1], "\"", sep = "") | ||
for (i in 2:length(var1)) { | ||
var1_i <- var1[i] | ||
var1_conc <- paste (var1_conc, paste (", \"", var1_i, "\"", sep = "")) | ||
} | ||
var1_conc <- paste (var1_conc, "]", sep = "") | ||
strprintline <- paste (strprintline, "\"feature\"",":\"", var1_conc,"\", ", sep = "") | ||
} | ||
} | ||
strprintline <- paste (strprintline, "\"feature.anchor\"",":\"", var2,"\", ", sep = "") | ||
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# var3 | ||
if (!is.null(var3)) { | ||
if (length(var3) == 1) { | ||
strprintline <- paste (strprintline, "\"show.attribute\":\"", var3, "\", ", sep = "") | ||
} else { | ||
var3_conc <- paste ("[\"", var3[1], "\"", sep = "") | ||
for (i in 2:length(var3)) { | ||
var3_i <- var3[i] | ||
var3_conc <- paste (var3_conc, paste (", \"", var3_i, "\"", sep = "")) | ||
} | ||
var3_conc <- paste (var3_conc, "]", sep = "") | ||
strprintline <- paste (strprintline, "\"feature\"",":\"", var3_conc,"\", ", sep = "") | ||
} | ||
} | ||
strprintline <- paste (strprintline, "\"internals\"",":\"", var4,"\", ", sep = "") | ||
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# var5 | ||
if (!is.null(var5)) { | ||
if (length(var5) == 1) { | ||
strprintline <- paste(strprintline, "\"filter.attribute\"",":\"", var5,"\", ", sep = "") | ||
} else { | ||
var5_conc <- paste ("[\"", var5[1], "\"", sep = "") | ||
for (i in 2:length(var5)) { | ||
var5_i <- var1[i] | ||
var5_conc <- paste (var5_conc, paste (", \"", var5_i, "\"", sep = "")) | ||
} | ||
var5_conc <- paste (var5_conc, "]", sep = "") | ||
strprintline <- paste (strprintline, "\"feature\"",":\"", var5_conc,"\", ", sep = "") | ||
} | ||
} | ||
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# var6 | ||
if (!is.null(var6)) { | ||
if (length(var6) == 1) { | ||
strprintline <- strprintline <- paste(strprintline, "\"attribute.value\"",":\"", var6, "\", ", sep = "") | ||
} else { | ||
var6_conc <- paste ("[\"", var6[1], "\"", sep = "") | ||
for (i in 2:length(var6)) { | ||
var6_i <- var6[i] | ||
var6_conc <- paste (var6_conc, paste (", \"", var6_i, "\"", sep = "")) | ||
} | ||
var6_conc <- paste (var6_conc, "]", sep = "") | ||
strprintline <- paste (strprintline, "\"feature\"",":\"", var6_conc,"\", ", sep = "") | ||
} | ||
} | ||
strprintline <- paste (strprintline, "\"strand\"",":\"", var7,"\", ", sep = "") | ||
strprintline <- paste (strprintline, "\"direction\"",":\"", var8,"\", ", sep = "") | ||
strprintline <- paste (strprintline, "\"distance\"",":","[",distance_up,", ",distance_down,"]", sep = "") | ||
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strprintline <- paste (strprintline, "}", sep = "") | ||
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return (strprintline) | ||
} | ||
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# Creating modules | ||
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# First module | ||
#-------------------------------- | ||
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# A module to read the inputs | ||
# UI-part | ||
PrintTablesUI <- function(id, strcol3_list, strcol9_list, label = "ui1UI") { | ||
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ns <- NS(id) | ||
shinyUI(fluidRow( | ||
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box(background = "light-blue", div(img(src="logo_MPIE_gr.png")),title= paste ("query ", gsub("c", "", id), sep = ""),width=2), | ||
box(background = "light-blue",title= "JSON_UROPA_queries", | ||
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column(width = 6, | ||
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sliderInput(ns("distance_up"), "distance_uptream", min = -100000, max = 100000,step=100, value = c(500)), | ||
bsTooltip(ns("distance_up"), "TEST IS THIS WORK?", "right", trigger = "hover"), | ||
#bsTooltip("distance_up", title = "use keyboard arrows",placement = "left", trigger = "hover"), | ||
selectInput(ns("var8"),"direction",choices=c("any_direction","upstream","downstream")), | ||
selectInput(ns("var4"),"internals",choices=c("none","center","any")), | ||
selectInput(ns("var1"), "feature",as.list(strcol3_list),multiple = T), | ||
selectInput(ns("var6"), "attribute.value",as.list(strcol9_list),multiple = T) | ||
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), | ||
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column(width = 6, | ||
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sliderInput(ns("distance_down"), "distance_downstream",min = -100000, max = 100000,step=100,value = c(500)), | ||
selectInput(ns("var7"),"strand",choices=c("+","-","both")), | ||
selectInput(ns("var2"),"feature.anchor",choices=c("start","center","end")), | ||
selectInput(ns("var3"), "show.attribute",as.list(strcol9_list),multiple = T), | ||
selectInput(ns("var5"), "filter.attribute",as.list(strcol9_list),multiple = T) | ||
) | ||
) | ||
)) | ||
} | ||
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# Server-part | ||
PrintTables <- function(input, output, session) { | ||
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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$distance_down}) | ||
) | ||
return(strinputvars) | ||
} | ||
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#================================ | ||
# | ||
# Program code | ||
# | ||
#================================ | ||
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# We'll save it in a variable `ui` so that we can preview it in the console | ||
ui <- dashboardPage( | ||
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dashboardHeader(title=div(img(src="site.logo.jpg"))), | ||
dashboardSidebar( | ||
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fluidRow( | ||
column(width=12, | ||
radioButtons("gtf_files" ,"Select tab-separated gtf file",choices= | ||
c("human_gencode.v22.gene"="gencode.v24.annotation.gtf", | ||
"mouse_gencode.vM5.genes"="gencode.vM5.genes.gtf", | ||
"other"="user_defined.gtf")), | ||
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actionButton("gftfile_upload", "Upload file"), | ||
fileInput("file1", "Upload bed File")), | ||
radioTooltip(id = "gtf_files", choice = "user_defined.gtf", | ||
title = "Please rename your gtf file as: user_defined.gtf", trigger = "hover"), | ||
column(width=12, | ||
selectInput("priority"," prioritized query",choices=c("FALSE","TRUE"))), | ||
column(width = 12, | ||
numericInput("NrQuery","Enter number of queries", 1, min=1, max=NaN), | ||
actionButton("addqueries", "Add queries")) | ||
) | ||
#title=div(img(src="logo_MPIE_gr.png")) | ||
), | ||
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dashboardBody( | ||
# div(img(src="logo_MPIE_gr.png")), | ||
##define slider color | ||
tags$style(HTML(".irs-bar {width: 100%; height: 10px; background: black; border-top: 1px solid black; border-bottom: 1px solid black;}")), | ||
tags$style(HTML(".irs-bar-edge {background: black; border: 1px solid black; height:10px; border-radius: 10px 10px 10px 10px;}")), | ||
tags$style(HTML(".irs-line {border: 1px solid black; height: 10px;}")), | ||
tags$style(HTML(".irs-grid-text {font-family: 'arial'; color: black}")), | ||
tags$style(HTML(".irs-max {font-family: 'arial'; color: black;}")), | ||
tags$style(HTML(".irs-min {font-family: 'arial'; color: black;}")), | ||
tags$style(HTML(".irs-single {color:black; background:#6666ff;}")), | ||
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uiOutput("testSlider"), | ||
#### end of define slider color | ||
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div(id = "ui_zero"), | ||
div(id = "ui_zero2"), | ||
actionButton("printres", "Save JSON format file",icon("paper-plane"), | ||
style="color: #fff; background-color: #337ab7; border-color: #2e6da4") | ||
) | ||
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) | ||
server <- (function(input, output, session) { | ||
options(shiny.maxRequestSize=30*1024*1024^2) | ||
output$textORdate <- renderUI({ | ||
}) | ||
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# read GTF file | ||
strcol3_list <- "test" | ||
strcol9_list <- "test" | ||
observeEvent(input$gftfile_upload, { | ||
#fread [,3][,9] library(data.table)fother | ||
dfgtffile <- as.data.frame(fread(input$gtf_files, sep = "\t", select = c(3, 9))) | ||
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strcol3_list <<- as.character(unique(sort(dfgtffile[,1]))) | ||
write.table (length(unique(dfgtffile[,2])), "test_0.txt", quote = F) | ||
#dfgtffile <- read.table("user_defined_SMALL.gtf", sep = "\t") | ||
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df_V3 <- gsub(pattern="; ",replacement="\t", unique(dfgtffile[,2]), fixed=TRUE) | ||
df_V3 <- gsub(pattern=" ",replacement="\t", df_V3, fixed=TRUE) | ||
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n <- length(df_V3) | ||
limit <- 10000 | ||
lowerlimit <- 1 | ||
keys <- "testval" | ||
write.table (length(unique(dfgtffile[,2])), "test_1.txt", quote = F) | ||
withProgress(message = 'Creating lists...', value = 0, { | ||
for (upperlimit in seq(limit, n, limit)) { | ||
df_V3_temp <- do.call(rbind.data.frame,strsplit(df_V3[lowerlimit:upperlimit],split="\t")) | ||
dfgtffile_ss1 <- df_V3_temp[,seq(1, ncol(df_V3_temp), 2)] | ||
keys <- unique(c(keys, as.vector(as.matrix(dfgtffile_ss1)))) | ||
lowerlimit <- lowerlimit + limit | ||
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incProgress(limit/n, detail = paste(upperlimit, " lines read.")) | ||
rm(df_V3_temp) | ||
rm (dfgtffile_ss1) | ||
} | ||
}) | ||
write.table (length(unique(dfgtffile[,2])), "test_2.txt", quote = F) | ||
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strcol9_list <<- keys | ||
write.table (dim(dfgtffile), "test_3.txt", quote = F) | ||
}) | ||
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# Print the tables (first module) | ||
observeEvent(input$addqueries, { | ||
for (counter in startpoint:input$NrQuery) { | ||
ID <- paste0("c", counter) | ||
insertUI("#ui_zero", "beforeEnd", PrintTablesUI(ID, strcol3_list, strcol9_list)) | ||
module_iterres <- callModule(PrintTables, ID) | ||
assign (paste("var_", ID, sep = ""), value = module_iterres, pos = 1) | ||
observeEvent(input$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$priority, "\",\n", | ||
"\"gtf\": \"", input$gtf_files, "\",\n", | ||
# toprint the path | ||
"\"bed\": \"", paste(input$file1$datapath, "\\", input$file1$name, sep = ""), "\"", sep = "", | ||
#to print the file name only | ||
# "\"bed\": \"", input$file1$name, "\"", sep = "", | ||
"}") | ||
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write.table (resline, "configuration_file.txt", quote = F, col.names = F, row.names = F) | ||
}) | ||
}) | ||
} | ||
}) | ||
}) | ||
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# Running the program | ||
shinyApp(ui = ui, server = server) | ||
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