R/splitReplicates.R
In charlottesirot/elementR: An Framework for Reducing Elemental LAICPMS Data from Solid Structures
Defines functions
splitReplicate
Documented in
splitReplicate
splitReplicate <- function(){
ui <- shinyUI(dashboardPage(
dashboardHeader(),
dashboardSidebar(),
dashboardBody(
tags$style(HTML("
.form-control.shiny-bound-input.shinyjs-resettable{
margin-bottom:30px
}"
)),
useShinyjs(),
uiOutput("start"),
uiOutput("graphics")
)
))
server <- shinyServer(function(input, output, session) {
addClass(selector = "body", class = "sidebar-collapse")
sampleNumber <- reactiveValues(temp = 0) #Number of hypothetized sample
fileSplitName <- reactiveValues(temp = NULL)
fileSplitData <- reactiveValues(temp = NULL)
plateauDelin <- reactiveValues(temp = NULL)
sampleLimits <- reactiveValues(temp = NULL)
colReplicates <- reactiveValues(temp = NULL)
standElem <- reactiveValues(temp = NULL)
output$start <- renderUI({
div(
box(
title = list(icon("folder-o"),"New Project"),
width = 6,
status="primary",
solidHeader = TRUE,
p("1. Choose the project folder"),
actionButton("createProjButton", "Create your project !"),
actionButton("runExampleNew", "Run Example")
),
box(
title = list(icon("folder"),"Settings"),
width = 6,
solidHeader = TRUE,
status="primary",
uiOutput("choiceStandardElement"),
uiOutput("numberSample")
)
)
})#end of start
output$numberSample <- renderUI({
numericInput("num", label = h4("Number of sampling"), value = sampleNumber$temp)
})
output$choiceStandardElement <- renderUI({
tempElement <- which(str_detect(colReplicates$temp, "Ca") == TRUE)
selectInput("standardElement", label = h4("Select your standard element"),
choices = colReplicates$temp,
selected = colReplicates$temp[tempElement])
})
##############################################################
# upload the file to split
##############################################################
observe({
if(!is.null(input$createProjButton)){
if(input$createProjButton != 0){
isolate({
if(Sys.info()[1] == "Windows"){
fileSplitName$temp <- choose.files(default = getwd())
} else {
fileSplitName$temp <- tk_choose.files(default = getwd(),
caption = "Select files",
multi = FALSE,
filters = matrix(c(".csv", ".csv"), 1,2),
index = 1)
}
})
}
}
}) #observe
observe({
if(!is.null(input$runExampleNew)){
if(input$runExampleNew != 0){
isolate({
if(Sys.info()[1] == "Windows"){
fileSplitName$temp <- paste0(system.file("", package="elementR"), "/splitReplicate_example.csv")
} else {
fileSplitName$temp <- paste0(system.file("", package="elementR"), "splitReplicate_example.csv")
}
})
}
}
}) #observe
##############################################################
# read the file to split
##############################################################
observe({
if(!is.null(fileSplitName$temp)){
isolate({
fileSplitData$temp <- readData(fileSplitName$temp, sep = ";", dec = ".")
colReplicates$temp <- colnames(fileSplitData$temp)
})
}
})
observe({
if(!is.null(input$standardElement)){
isolate({
standElem$temp <- which(colnames(fileSplitData$temp) == input$standardElement)
})
}
})
observe({
if(!is.null(fileSplitName$temp) & length(standElem$temp) != 0){
isolate({
sampleNumber$temp <- 0
sampleLimits$temp <- NULL
plateauDelin$temp <- kmeans(fileSplitData$temp[, standElem$temp], 2, algorithm = "Hartigan-Wong")$cluster
deux <- fileSplitData$temp[which(plateauDelin$temp == 2)[1], standElem$temp]
un <- fileSplitData$temp[which(plateauDelin$temp == 1)[1], standElem$temp]
if(un > deux){
plateauDelin$temp <- 2 - plateauDelin$temp
} else {
plateauDelin$temp <- plateauDelin$temp - 1
}
tempLimits <- vector()
if(plateauDelin$temp[1] == 1){
tempLimits <- c(tempLimits, 1)
sampleNumber$temp <- 1
} else {
sampleNumber$temp <- 0
}
for(i in 3:(length(plateauDelin$temp)-1)){
if(plateauDelin$temp[i] == 1 & plateauDelin$temp[i-1] == 0 & plateauDelin$temp[i-2] == 0 & plateauDelin$temp[i+1] == 1 & plateauDelin$temp[i+2] == 1){
sampleNumber$temp <- sampleNumber$temp +1
tempLimits <- c(tempLimits, i)
} else if(plateauDelin$temp[i] == 0 & plateauDelin$temp[i-1] == 1 & plateauDelin$temp[i-2] == 1 & plateauDelin$temp[i+1] == 0 & plateauDelin$temp[i+2] == 0){
tempLimits <- c(tempLimits, i)
} else {}
}
new <- tempLimits
if(sampleNumber$temp > 2){
for(i in 2:(length(tempLimits)-1)){
if(!is.na(tempLimits[i]) & !is.na(tempLimits[i+1])){
if(tempLimits[i] == (tempLimits[i+1]-1)){
new <- new[-c(i,i+1)]
sampleNumber$temp <- sampleNumber$temp - 1
} else {}
} else{}
}
for(i in 1:length(new)){
if(i == 1){
if(new[1] != 1){
new[1] <- new[1] - floor(new[1]/3)
}
} else {
if(i%%2 == 0){
new[i] <- new[i] + floor((new[i+1]-new[i])/3)
} else {
new[i] <- new[i] - floor((new[i]-new[i-1])/3)
}
}
}
sampleLimits$temp <- new
} else {}
})
}
})
##############################################################
# plot the graphics
##############################################################
output$graphics <- renderUI({
input$standardElement
if(!is.null(fileSplitName$temp) & length(standElem$temp) != 0){
minX <- min(fileSplitData$temp[,1], na.rm = TRUE)
maxX <- max(fileSplitData$temp[,1], na.rm = TRUE)
column(12, style = "padding-right: 5px",
box(
title = list(icon("share"),"Data to split"),
status="primary",
solidHeader = TRUE,
width = "100%",
fluidRow(
column(10,
plotOutput("rawDataPlot"),
lapply(1:input$num, function(i){
limitLow <- sampleLimits$temp[2*i-1]
limitHigh <- sampleLimits$temp[2*i]
div(style="height: 82px;padding-left: 40px",
sliderInput(paste0("tag",i),paste0("Replicates", i, "limits"), value = c(fileSplitData$temp[limitLow,1],fileSplitData$temp[limitHigh,1] ), min = minX, max = maxX, step = 1, width = '100%', round = TRUE)
)
})
),
column(2, style = "margin-top:370px",
actionButton("exportReplicates", "Export the replicates"),
lapply(1:input$num, function(i){
textInput(paste0("name",i), label = "", value = paste0("Replicate_", i))
})
)
)
)
)
} else { NULL}
})# end of graphics
output$rawDataPlot <- renderPlot({
input$standardElement
par(mar = c(3,3.5,1.75,0))
if(!is.null(fileSplitName$temp) & !is.null(sampleNumber$temp) & length(standElem$temp) != 0){
maxY <- max(fileSplitData$temp[,standElem$temp], na.rm = TRUE)
minX <- min(fileSplitData$temp[,1], na.rm = TRUE)
maxX <- max(fileSplitData$temp[,1], na.rm = TRUE)
plot(fileSplitData$temp[, standElem$temp] ~ fileSplitData$temp[,1], xlim = c(minX, maxX), ylim = c(0,maxY), ylab = "cps/s", type = "l")
lapply(1:input$num, function(i){
abline(v = eval(parse(text = paste0("input$tag", i)))[1], lty = "dashed", col = "grey", lwd = 2)
abline(v = eval(parse(text = paste0("input$tag", i)))[2], lty = "dashed", col = "grey", lwd = 2)
if(!is.null(eval(parse(text = paste0("input$tag", i))))){
rect(eval(parse(text = paste0("input$tag", i)))[1], -maxY, eval(parse(text = paste0("input$tag", i)))[2], (1+10/100)*maxY, col = "#8B735564", border = NA)
}
})
} else {NULL}
})
##############################################################
# Export the split data
##############################################################
observe({
if(!is.null(input$exportReplicates)){
if(input$exportReplicates > 0){
isolate({
if(Sys.info()[1] == "Windows"){
projPath <- choose.dir()
} else {
projPath <- tk_choose.dir()
}
if(!is.na(projPath)){
lapply(1:input$num, function(i){
limits <- which(fileSplitData$temp[,1] >= eval(parse(text = paste0("input$tag", i)))[1] & fileSplitData$temp[,1] <= eval(parse(text = paste0("input$tag", i)))[2])
tabTemp <- fileSplitData$temp[limits,]
write.csv(tabTemp, file = paste0(projPath, "/", eval(parse(text = paste0("input$name", i))), ".csv"))
})
res <- tkmessageBox(title = "INFO !",message = "data exported", icon = "info", type = "ok")
}
})
}
}
})
})
app <- shinyApp(ui, server)
runApp(app, launch.browser = TRUE)
}
charlottesirot/elementR documentation built on March 8, 2024, 5:13 a.m.
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Defines functions splitReplicate
Documented in splitReplicate
splitReplicate <- function(){
ui <- shinyUI(dashboardPage(
dashboardHeader(),
dashboardSidebar(),
dashboardBody(
tags$style(HTML("
.form-control.shiny-bound-input.shinyjs-resettable{
margin-bottom:30px
}"
)),
useShinyjs(),
uiOutput("start"),
uiOutput("graphics")
)
))
server <- shinyServer(function(input, output, session) {
addClass(selector = "body", class = "sidebar-collapse")
sampleNumber <- reactiveValues(temp = 0) #Number of hypothetized sample
fileSplitName <- reactiveValues(temp = NULL)
fileSplitData <- reactiveValues(temp = NULL)
plateauDelin <- reactiveValues(temp = NULL)
sampleLimits <- reactiveValues(temp = NULL)
colReplicates <- reactiveValues(temp = NULL)
standElem <- reactiveValues(temp = NULL)
output$start <- renderUI({
div(
box(
title = list(icon("folder-o"),"New Project"),
width = 6,
status="primary",
solidHeader = TRUE,
p("1. Choose the project folder"),
actionButton("createProjButton", "Create your project !"),
actionButton("runExampleNew", "Run Example")
),
box(
title = list(icon("folder"),"Settings"),
width = 6,
solidHeader = TRUE,
status="primary",
uiOutput("choiceStandardElement"),
uiOutput("numberSample")
)
)
})#end of start
output$numberSample <- renderUI({
numericInput("num", label = h4("Number of sampling"), value = sampleNumber$temp)
})
output$choiceStandardElement <- renderUI({
tempElement <- which(str_detect(colReplicates$temp, "Ca") == TRUE)
selectInput("standardElement", label = h4("Select your standard element"),
choices = colReplicates$temp,
selected = colReplicates$temp[tempElement])
})
##############################################################
# upload the file to split
##############################################################
observe({
if(!is.null(input$createProjButton)){
if(input$createProjButton != 0){
isolate({
if(Sys.info()[1] == "Windows"){
fileSplitName$temp <- choose.files(default = getwd())
} else {
fileSplitName$temp <- tk_choose.files(default = getwd(),
caption = "Select files",
multi = FALSE,
filters = matrix(c(".csv", ".csv"), 1,2),
index = 1)
}
})
}
}
}) #observe
observe({
if(!is.null(input$runExampleNew)){
if(input$runExampleNew != 0){
isolate({
if(Sys.info()[1] == "Windows"){
fileSplitName$temp <- paste0(system.file("", package="elementR"), "/splitReplicate_example.csv")
} else {
fileSplitName$temp <- paste0(system.file("", package="elementR"), "splitReplicate_example.csv")
}
})
}
}
}) #observe
##############################################################
# read the file to split
##############################################################
observe({
if(!is.null(fileSplitName$temp)){
isolate({
fileSplitData$temp <- readData(fileSplitName$temp, sep = ";", dec = ".")
colReplicates$temp <- colnames(fileSplitData$temp)
})
}
})
observe({
if(!is.null(input$standardElement)){
isolate({
standElem$temp <- which(colnames(fileSplitData$temp) == input$standardElement)
})
}
})
observe({
if(!is.null(fileSplitName$temp) & length(standElem$temp) != 0){
isolate({
sampleNumber$temp <- 0
sampleLimits$temp <- NULL
plateauDelin$temp <- kmeans(fileSplitData$temp[, standElem$temp], 2, algorithm = "Hartigan-Wong")$cluster
deux <- fileSplitData$temp[which(plateauDelin$temp == 2)[1], standElem$temp]
un <- fileSplitData$temp[which(plateauDelin$temp == 1)[1], standElem$temp]
if(un > deux){
plateauDelin$temp <- 2 - plateauDelin$temp
} else {
plateauDelin$temp <- plateauDelin$temp - 1
}
tempLimits <- vector()
if(plateauDelin$temp[1] == 1){
tempLimits <- c(tempLimits, 1)
sampleNumber$temp <- 1
} else {
sampleNumber$temp <- 0
}
for(i in 3:(length(plateauDelin$temp)-1)){
if(plateauDelin$temp[i] == 1 & plateauDelin$temp[i-1] == 0 & plateauDelin$temp[i-2] == 0 & plateauDelin$temp[i+1] == 1 & plateauDelin$temp[i+2] == 1){
sampleNumber$temp <- sampleNumber$temp +1
tempLimits <- c(tempLimits, i)
} else if(plateauDelin$temp[i] == 0 & plateauDelin$temp[i-1] == 1 & plateauDelin$temp[i-2] == 1 & plateauDelin$temp[i+1] == 0 & plateauDelin$temp[i+2] == 0){
tempLimits <- c(tempLimits, i)
} else {}
}
new <- tempLimits
if(sampleNumber$temp > 2){
for(i in 2:(length(tempLimits)-1)){
if(!is.na(tempLimits[i]) & !is.na(tempLimits[i+1])){
if(tempLimits[i] == (tempLimits[i+1]-1)){
new <- new[-c(i,i+1)]
sampleNumber$temp <- sampleNumber$temp - 1
} else {}
} else{}
}
for(i in 1:length(new)){
if(i == 1){
if(new[1] != 1){
new[1] <- new[1] - floor(new[1]/3)
}
} else {
if(i%%2 == 0){
new[i] <- new[i] + floor((new[i+1]-new[i])/3)
} else {
new[i] <- new[i] - floor((new[i]-new[i-1])/3)
}
}
}
sampleLimits$temp <- new
} else {}
})
}
})
##############################################################
# plot the graphics
##############################################################
output$graphics <- renderUI({
input$standardElement
if(!is.null(fileSplitName$temp) & length(standElem$temp) != 0){
minX <- min(fileSplitData$temp[,1], na.rm = TRUE)
maxX <- max(fileSplitData$temp[,1], na.rm = TRUE)
column(12, style = "padding-right: 5px",
box(
title = list(icon("share"),"Data to split"),
status="primary",
solidHeader = TRUE,
width = "100%",
fluidRow(
column(10,
plotOutput("rawDataPlot"),
lapply(1:input$num, function(i){
limitLow <- sampleLimits$temp[2*i-1]
limitHigh <- sampleLimits$temp[2*i]
div(style="height: 82px;padding-left: 40px",
sliderInput(paste0("tag",i),paste0("Replicates", i, "limits"), value = c(fileSplitData$temp[limitLow,1],fileSplitData$temp[limitHigh,1] ), min = minX, max = maxX, step = 1, width = '100%', round = TRUE)
)
})
),
column(2, style = "margin-top:370px",
actionButton("exportReplicates", "Export the replicates"),
lapply(1:input$num, function(i){
textInput(paste0("name",i), label = "", value = paste0("Replicate_", i))
})
)
)
)
)
} else { NULL}
})# end of graphics
output$rawDataPlot <- renderPlot({
input$standardElement
par(mar = c(3,3.5,1.75,0))
if(!is.null(fileSplitName$temp) & !is.null(sampleNumber$temp) & length(standElem$temp) != 0){
maxY <- max(fileSplitData$temp[,standElem$temp], na.rm = TRUE)
minX <- min(fileSplitData$temp[,1], na.rm = TRUE)
maxX <- max(fileSplitData$temp[,1], na.rm = TRUE)
plot(fileSplitData$temp[, standElem$temp] ~ fileSplitData$temp[,1], xlim = c(minX, maxX), ylim = c(0,maxY), ylab = "cps/s", type = "l")
lapply(1:input$num, function(i){
abline(v = eval(parse(text = paste0("input$tag", i)))[1], lty = "dashed", col = "grey", lwd = 2)
abline(v = eval(parse(text = paste0("input$tag", i)))[2], lty = "dashed", col = "grey", lwd = 2)
if(!is.null(eval(parse(text = paste0("input$tag", i))))){
rect(eval(parse(text = paste0("input$tag", i)))[1], -maxY, eval(parse(text = paste0("input$tag", i)))[2], (1+10/100)*maxY, col = "#8B735564", border = NA)
}
})
} else {NULL}
})
##############################################################
# Export the split data
##############################################################
observe({
if(!is.null(input$exportReplicates)){
if(input$exportReplicates > 0){
isolate({
if(Sys.info()[1] == "Windows"){
projPath <- choose.dir()
} else {
projPath <- tk_choose.dir()
}
if(!is.na(projPath)){
lapply(1:input$num, function(i){
limits <- which(fileSplitData$temp[,1] >= eval(parse(text = paste0("input$tag", i)))[1] & fileSplitData$temp[,1] <= eval(parse(text = paste0("input$tag", i)))[2])
tabTemp <- fileSplitData$temp[limits,]
write.csv(tabTemp, file = paste0(projPath, "/", eval(parse(text = paste0("input$name", i))), ".csv"))
})
res <- tkmessageBox(title = "INFO !",message = "data exported", icon = "info", type = "ok")
}
})
}
}
})
})
app <- shinyApp(ui, server)
runApp(app, launch.browser = TRUE)
}
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