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JSON_UROPA/20170721_JSON_UROPA_query.R
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#================================ | |
# | |
# Initialization | |
# | |
#================================ | |
# Loading in libraries | |
library(shiny) | |
library(shinydashboard) | |
library(shinyBS) | |
library(data.table) | |
library(readr) | |
##### define popover for radiobuttons in the sidebar | |
radioTooltip <- function(id, choice, title, placement = "bottom", trigger = "hover", options = NULL){ | |
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'); | |
$(this.parentElement).tooltip(opts); | |
} | |
}) | |
}, 500) | |
}); | |
"))) | |
htmltools::attachDependencies(bsTag, shinyBS:::shinyBSDep) | |
} | |
########### end of define popover for radiobuttons in the sidebar | |
# Defining the parameters | |
startpoint <- 1 | |
# User-defined functions | |
fileInput2 <- function(inputId, label = NULL, labelIcon = NULL, multiple = FALSE, | |
accept = NULL, width = NULL, progress = TRUE, ...) { | |
# add class fileinput_2 defined in UI to hide the inputTag | |
inputTag <- tags$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 = ",") | |
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") | |
) | |
) | |
} | |
# A print function to create the configuration file format | |
JU_resformat <- function (var1, var2, var3, var4, var5, var6, var7, var8, distance_up, distance_down) { | |
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 = "") | |
# 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 = "") | |
# 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 = "") | |
} | |
} | |
# 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 = "") | |
strprintline <- paste (strprintline, "}", sep = "") | |
return (strprintline) | |
} | |
# Creating modules | |
# First module | |
#-------------------------------- | |
# A module to read the inputs | |
# UI-part | |
PrintTablesUI <- function(id, strcol3_list, strcol9_list, label = "ui1UI") { | |
ns <- NS(id) | |
shinyUI(fluidRow( | |
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", | |
column(width = 6, | |
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) | |
), | |
column(width = 6, | |
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) | |
) | |
) | |
)) | |
} | |
# 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$distance_down}) | |
) | |
return(strinputvars) | |
} | |
#================================ | |
# | |
# Program code | |
# | |
#================================ | |
# We'll save it in a variable `ui` so that we can preview it in the console | |
ui <- dashboardPage( | |
dashboardHeader(title=div(img(src="site.logo.jpg"))), | |
dashboardSidebar( | |
fluidRow( | |
column(width=12, | |
radioButtons("gtf_files" ,"Select tab-separated gtf file",choices= | |
c("human_gencode.v22.gene"="gencode.v24.annotation.gtf", | |
"mouse_gencode.vM5.genes"="gencode.vM5.genes.gtf", | |
"other"="user_defined.gtf")), | |
actionButton("gftfile_upload", "Upload file"), | |
fileInput("file1", "Upload bed File")), | |
radioTooltip(id = "gtf_files", choice = "user_defined.gtf", | |
title = "Please rename your gtf file as: user_defined.gtf", trigger = "hover"), | |
column(width=12, | |
selectInput("priority"," prioritized query",choices=c("FALSE","TRUE"))), | |
column(width = 12, | |
numericInput("NrQuery","Enter number of queries", 1, min=1, max=NaN), | |
actionButton("addqueries", "Add queries")) | |
) | |
#title=div(img(src="logo_MPIE_gr.png")) | |
), | |
dashboardBody( | |
# div(img(src="logo_MPIE_gr.png")), | |
##define slider color | |
tags$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;}")), | |
uiOutput("testSlider"), | |
#### end of define slider color | |
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") | |
) | |
) | |
server <- (function(input, output, session) { | |
options(shiny.maxRequestSize=30*1024*1024^2) | |
output$textORdate <- renderUI({ | |
}) | |
# read GTF file | |
strcol3_list <- "test" | |
strcol9_list <- "test" | |
observeEvent(input$gftfile_upload, { | |
#fread [,3][,9] library(data.table)fother | |
dfgtffile <- as.data.frame(fread(input$gtf_files, sep = "\t", select = c(3, 9))) | |
strcol3_list <<- as.character(unique(sort(dfgtffile[,1]))) | |
write.table (length(unique(dfgtffile[,2])), "test_0.txt", quote = F) | |
#dfgtffile <- read.table("user_defined_SMALL.gtf", sep = "\t") | |
df_V3 <- gsub(pattern="; ",replacement="\t", unique(dfgtffile[,2]), fixed=TRUE) | |
df_V3 <- gsub(pattern=" ",replacement="\t", df_V3, fixed=TRUE) | |
n <- length(df_V3) | |
limit <- 10000 | |
lowerlimit <- 1 | |
keys <- "testval" | |
write.table (length(unique(dfgtffile[,2])), "test_1.txt", quote = F) | |
withProgress(message = 'Creating lists...', value = 0, { | |
for (upperlimit in seq(limit, n, limit)) { | |
df_V3_temp <- do.call(rbind.data.frame,strsplit(df_V3[lowerlimit:upperlimit],split="\t")) | |
dfgtffile_ss1 <- df_V3_temp[,seq(1, ncol(df_V3_temp), 2)] | |
keys <- unique(c(keys, as.vector(as.matrix(dfgtffile_ss1)))) | |
lowerlimit <- lowerlimit + limit | |
incProgress(limit/n, detail = paste(upperlimit, " lines read.")) | |
rm(df_V3_temp) | |
rm (dfgtffile_ss1) | |
} | |
}) | |
write.table (length(unique(dfgtffile[,2])), "test_2.txt", quote = F) | |
strcol9_list <<- keys | |
write.table (dim(dfgtffile), "test_3.txt", quote = F) | |
}) | |
# Print the tables (first module) | |
observeEvent(input$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 = "", | |
"}") | |
write.table (resline, "configuration_file.txt", quote = F, col.names = F, row.names = F) | |
}) | |
}) | |
} | |
}) | |
}) | |
# Running the program | |
shinyApp(ui = ui, server = server) | |