Nothing
cal_server <- function( input, output, session ) {
###### FIRST TAB
oldpar <- par(no.readonly = TRUE)
on.exit(par(oldpar))
oldopt <- options()
on.exit(options(oldopt))
options(shiny.maxRequestSize=100*1024^2) #file can be up to 50 mb; default is 5 mb
## initializations
shinyImageFile <- reactiveValues(shiny_img_origin = NULL, shiny_img_cropped = NULL,
shiny_img_final = NULL, Threshold = NULL)
IntensData <- NULL
ExpInfo <- NULL
MergedData <- NULL
FILENAME <- NULL
fit <- NULL
modelPlot <- NULL
LOB <- NULL
LOD <- NULL
LOQ <- NULL
predFunc <- NULL
CalibrationData <- NULL
startAutosave <- reactiveVal(value=FALSE)
#checks upload for file input
observe({
#default: upload image
if(input$upload == 1){
output$plot1 <- renderPlot({
if(is.null(input$file1)) {
output$rotatePanel <- renderUI({})
}
validate(need(!is.null(input$file1), "Must upload a valid jpg, png, or tiff"))
})
}
if(input$upload == 2){
# using sample image
img <- readImage(system.file("images", "sample.TIF", package="LFApp"))
shinyImageFile$shiny_img_origin <- img
shinyImageFile$shiny_img_cropped <- img
shinyImageFile$shiny_img_final <- img
shinyImageFile$filename <- "sample.TIF"
#outputs image to plot1 -- main plot
output$plot1 <- renderPlot({ EBImage::display(shinyImageFile$shiny_img_final, method = "raster") })
drawRotatePanel()
}
}) # end of observe
# NOTE renameUpload is completely unecessary. The app works without it perfectly.
# #the datapath is different from the one needed to properly recognize photo
# #so this function renames the file
# renameUpload <- function(inFile){
# if(is.null(inFile))
# return(NULL)
#
# oldNames <- inFile$datapath
# newNames <- file.path(dirname(inFile$datapath), inFile$name)
# file.rename(from = oldNames, to = newNames)
# inFile$datapath <- newNames
#
# return(inFile$datapath)
# }
#if they enter a new file, their file will become the new imageFile
observeEvent(input$file1, {
shinyImageFile$filename <- input$file1$name
# img <- readImage(renameUpload(input$file1)) # Commented it, because I think its redundant.
img <- readImage(input$file1$datapath)
shinyImageFile$shiny_img_origin <- img
shinyImageFile$shiny_img_cropped <- img
shinyImageFile$shiny_img_final <- img
output$plot1 <- renderPlot({EBImage::display(img, method = "raster")})
drawRotatePanel()
})
# NOTE This function draws rotation panel.
drawRotatePanel <- function() {
output$rotatePanel <- renderUI({
tagList(
sliderInput("rotate", "Rotate image",
min=-45, max=45, value=0),
actionButton("rotateCCW", "-90"),
actionButton("rotateCW", "+90"),
actionButton("fliphor", "FH"),
actionButton("flipver", "FV"),
)
})
}
observe({reactiveRotation()})
reactiveRotation <- eventReactive(input$rotate, {
isolate({
if (!is.null(shinyImageFile$shiny_img_cropped)) {
shinyImageFile$shiny_img_final <- EBImage::rotate(shinyImageFile$shiny_img_cropped, input$rotate,
bg.col="white")
output$plot1 <- renderPlot({EBImage::display(shinyImageFile$shiny_img_final, method = "raster")})
session$resetBrush("plot_brush")
}
})
})
observe({reactiveRotationCCW()})
reactiveRotationCCW <- eventReactive(input$rotateCCW, {
isolate({
if (!is.null(shinyImageFile$shiny_img_cropped)) {
shinyImageFile$shiny_img_cropped <- EBImage::rotate(shinyImageFile$shiny_img_cropped, -90)
shinyImageFile$shiny_img_final <- shinyImageFile$shiny_img_cropped
output$plot1 <- renderPlot({EBImage::display(shinyImageFile$shiny_img_final, method = "raster")})
session$resetBrush("plot_brush")
}
})
})
observe({reactiveRotationCW()})
reactiveRotationCW <- eventReactive(input$rotateCW, {
isolate({
if (!is.null(shinyImageFile$shiny_img_cropped)) {
shinyImageFile$shiny_img_cropped <- EBImage::rotate(shinyImageFile$shiny_img_cropped, 90)
shinyImageFile$shiny_img_final <- shinyImageFile$shiny_img_cropped
output$plot1 <- renderPlot({EBImage::display(shinyImageFile$shiny_img_final, method = "raster")})
session$resetBrush("plot_brush")
}
})
})
observe({reactiveRotationFlip()})
reactiveRotationFlip <- eventReactive(input$fliphor, {
isolate({
if (!is.null(shinyImageFile$shiny_img_cropped)) {
shinyImageFile$shiny_img_cropped <- EBImage::flip(shinyImageFile$shiny_img_cropped)
shinyImageFile$shiny_img_final <- shinyImageFile$shiny_img_cropped
output$plot1 <- renderPlot({EBImage::display(shinyImageFile$shiny_img_final, method = "raster")})
session$resetBrush("plot_brush")
}
})
})
observe({reactiveRotationFlop()})
reactiveRotationFlop <- eventReactive(input$flipver, {
isolate({
if (!is.null(shinyImageFile$shiny_img_cropped)) {
shinyImageFile$shiny_img_cropped <- EBImage::flop(shinyImageFile$shiny_img_cropped)
shinyImageFile$shiny_img_final <- shinyImageFile$shiny_img_cropped
output$plot1 <- renderPlot({EBImage::display(shinyImageFile$shiny_img_final, method = "raster")})
session$resetBrush("plot_brush")
}
})
})
croppedImage <- function(image, xmin, ymin, xmax, ymax){
if(length(dim(image)) == 2)
image <- image[xmin:xmax, ymin:ymax, drop = FALSE]
else if(length(dim(image)) == 3)
image <- image[xmin:xmax, ymin:ymax, ,drop = FALSE]
return(image)
}
observe({resetImage()})
resetImage <- eventReactive(input$reset,{
isolate({
# For now, resetting only the grid is enough. If there is a need of resseting the image
# and rotation settings, uncommennt following three lines.
shinyImageFile$shiny_img_cropped <- shinyImageFile$shiny_img_origin
shinyImageFile$shiny_img_final <- shinyImageFile$shiny_img_cropped
output$plot1 <- renderPlot({EBImage::display(shinyImageFile$shiny_img_final, method = "raster")})
session$resetBrush("plot_brush")
updateSliderInput(session, "rotate", value=0)
shinyjs::disable("segmentation")
})
})
#prompts shiny to look at recursive crop
observe({recursiveCrop()})
#only executes when keep is clicked
recursiveCrop <- eventReactive(input$plot_dblclick,{
isolate({
p <- input$plot_brush
validate(need(p$xmax <= dim(shinyImageFile$shiny_img_cropped)[1],
"Highlighted portion is out of bounds on the x-axis"))
validate(need(p$ymax <= dim(shinyImageFile$shiny_img_cropped)[2],
"Highlighted portion is out of bounds on the y-axis"))
validate(need(p$xmin >= 0,
"Highlighted portion is out of bounds on the x-axis"))
validate(need(p$ymin >= 0,
"Highlighted portion is out of bounds on the y-axis"))
shinyImageFile$shiny_img_cropped <- croppedImage(shinyImageFile$shiny_img_final, p$xmin, p$ymin, p$xmax, p$ymax)
shinyImageFile$shiny_img_final <- shinyImageFile$shiny_img_cropped
output$plot1 <- renderPlot({
EBImage::display(shinyImageFile$shiny_img_final, method = "raster")
})
updateSliderInput(session, "rotate", value=0)
session$resetBrush("plot_brush")
shinyjs::enable("reset")
})
session$resetBrush("plot_brush")
shinyjs::disable("segmentation")
})
observe({recursiveGrid()})
recursiveGrid <- eventReactive(input$plot_brush,{
isolate({
p <- input$plot_brush
output$plot1 <- renderPlot({
EBImage::display(shinyImageFile$shiny_img_final, method = "raster")
colcuts <- seq(p$xmin, p$xmax, length.out = input$strips + 1)
rowcuts <- seq(p$ymin, p$ymax, length.out = 2*input$bands) # bands + spaces between bands
for (x in colcuts) {
lines(x = rep(x, 2), y = c(p$ymin, p$ymax), col="red")
}
for (y in rowcuts) {
lines(x = c(p$xmin, p$xmax), y = rep(y, 2), col="red")
}
})
shinyjs::enable("reset")
shinyjs::enable("segmentation")
})
})
observe({recursiveSegmentation()})
#only executes when Apply Segmentation is clicked
recursiveSegmentation <- eventReactive(input$segmentation,{
isolate({
p <- input$plot_brush
# Check if the region of interest is out of the bounds
if (p$xmax <= dim(shinyImageFile$shiny_img_cropped)[1] &&
p$ymax <= dim(shinyImageFile$shiny_img_cropped)[2] &&
p$xmin >= 0 &&
p$ymin >= 0) {
MAX <- dim(shinyImageFile$shiny_img_cropped)[1:2]
colcuts <- seq(p$xmin, p$xmax, length.out = input$strips + 1)
rowcuts <- seq(p$ymin, p$ymax, length.out = 2*input$bands)
segmentation.list <- vector("list", length = input$strips)
count <- 0
for(i in 1:input$strips){
tmp.list <- vector("list", length = 2*input$bands-1)
for(j in 1:(2*input$bands-1)){
img <- shinyImageFile$shiny_img_final
if(length(dim(img)) == 2)
img <- img[colcuts[i]:colcuts[i+1], rowcuts[j]:rowcuts[j+1]]
else if(length(dim(img)) == 3)
img <- img[colcuts[i]:colcuts[i+1], rowcuts[j]:rowcuts[j+1], , drop = FALSE]
tmp.list[[j]] <- img
}
segmentation.list[[i]] <- tmp.list
}
shinyImageFile$cropping_grid <- list("columns" = colcuts, "rows" = rowcuts)
shinyImageFile$segmentation_list <- segmentation.list
updateTabsetPanel(session, "tabs", selected = "tab2")
} else {
showNotification("Error: The grid is out of bounds", duration = 5, type="error")
}
})
})
################# END OF THE FIRST TAB
############### SECOND TAB
observe({
input$thresh
updateNumericInput(session, "selectStrip", max=input$strips)
})
observe({input$channel})
observe({recursiveThreshold()})
recursiveThreshold <- eventReactive(input$threshold,{
isolate({
seg.list <- shinyImageFile$segmentation_list
i <- input$selectStrip
if(input$thresh == 2){
Background <- vector(mode = "list", length = input$bands)
for(j in 1:input$bands){
img <- seg.list[[i]][[j]]
if(colorMode(img) > 0){
img <- 1-EBImage::channel(img, input$channel)
}
if(input$invert) {
img <- 1 - img
}
Background[[j]] <- as.numeric(EBImage::imageData(img))
}
Background.Threshold <- quantile(unlist(Background),
probs = input$quantile1/100)
shinyImageFile$Threshold <- Background.Threshold
output$plot3 <- renderPlot({
par(mfcol = c(1, input$bands))
Bands <- seq(1, 2*input$bands-1, by = 2)
count <- 0
for(j in Bands){
count <- count + 1
img <- seg.list[[i]][[j]]
if(colorMode(img) > 0){
img <- 1-EBImage::channel(img, input$channel)
}
if(input$invert) {
img <- 1 - img
}
signal <- EBImage::imageData(img) > Background.Threshold
EBImage::imageData(img) <- signal
plot(img)
title(paste0("Line ", count))
}
})
shinyImageFile$Mean_Intensities <- matrix(0, nrow = 1, ncol = input$bands)
shinyImageFile$Median_Intensities <- matrix(0, nrow = 1, ncol = input$bands)
output$plot4 <- renderPlot({
par(mfcol = c(1, input$bands))
count <- 0
Bands <- seq(1, 2*input$bands-1, by = 2)
count <- 0
for(j in Bands){
count <- count + 1
img <- seg.list[[i]][[j]]
if(colorMode(img) > 0){
img <- 1-EBImage::channel(img, input$channel)
}
if(input$invert) {
img <- 1 - img
}
signal <- EBImage::imageData(img) > Background.Threshold
EBImage::imageData(img) <- (EBImage::imageData(img) - Background.Threshold)*signal
shinyImageFile$Mean_Intensities[1,count] <- mean(EBImage::imageData(img)[signal])
shinyImageFile$Median_Intensities[1,count] <- median(EBImage::imageData(img)[signal])
plot(img)
title(paste0("Line ", count))
}
})
}
else if(input$thresh == 1){
Background.Threshold <- numeric(input$bands)
output$plot3 <- renderPlot({
par(mfcol = c(1, input$bands))
count1 <- 0
Bands <- seq(1, 2*input$bands-1, by = 2)
count2 <- 0
for(j in Bands){
count1 <- count1 + 1
count2 <- count2 + 1
img <- seg.list[[i]][[j]]
if(colorMode(img) > 0){
img <- 1-EBImage::channel(img, input$channel)
}
if(input$invert) {
img <- 1 - img
}
Background.Threshold[count1] <- otsu(img)
signal <- EBImage::imageData(img) > Background.Threshold[count1]
EBImage::imageData(img) <- signal
plot(img)
title(paste0("Line ", count2))
}
shinyImageFile$Threshold <- Background.Threshold
})
shinyImageFile$Mean_Intensities <- matrix(0, nrow = 1, ncol = input$bands)
shinyImageFile$Median_Intensities <- matrix(0, nrow = 1, ncol = input$bands)
output$plot4 <- renderPlot({
par(mfcol = c(1, input$bands))
count1 <- 0
Bands <- seq(1, 2*input$bands-1, by = 2)
count2 <- 0
for(j in Bands){
count1 <- count1 + 1
count2 <- count2 + 1
img <- seg.list[[i]][[j]]
if(colorMode(img) > 0){
img <- 1-EBImage::channel(img, input$channel)
}
if(input$invert) {
img <- 1 - img
}
thr <- otsu(img)
signal <- EBImage::imageData(img) > thr
EBImage::imageData(img) <- (EBImage::imageData(img) - thr)*signal
shinyImageFile$Mean_Intensities[1,count1] <- mean(EBImage::imageData(img)[signal])
shinyImageFile$Median_Intensities[1,count1] <- median(EBImage::imageData(img)[signal])
plot(img)
title(paste0("Line ", count2))
}
})
}
else if(input$thresh == 3){
Background.Threshold <- numeric(input$bands)
output$plot3 <- renderPlot({
par(mfcol = c(1, input$bands))
count1 <- 0
Bands <- seq(1, 2*input$bands-1, by = 2)
count2 <- 0
for(j in Bands){
count1 <- count1 + 1
count2 <- count2 + 1
img <- seg.list[[i]][[j]]
if(colorMode(img) > 0){
img <- 1-EBImage::channel(img, input$channel)
}
if(input$invert) {
img <- 1 - img
}
Background.Threshold[count1] <- triangle(img, input$tri_offset)
signal <- EBImage::imageData(img) > Background.Threshold[count1]
EBImage::imageData(img) <- signal
plot(img)
title(paste0("Line ", count2))
}
shinyImageFile$Threshold <- Background.Threshold
})
shinyImageFile$Mean_Intensities <- matrix(0, nrow = 1, ncol = input$bands)
shinyImageFile$Median_Intensities <- matrix(0, nrow = 1, ncol = input$bands)
output$plot4 <- renderPlot({
par(mfcol = c(1, input$bands))
count1 <- 0
Bands <- seq(1, 2*input$bands-1, by = 2)
count2 <- 0
for(j in Bands){
count1 <- count1 + 1
count2 <- count2 + 1
img <- seg.list[[i]][[j]]
if(colorMode(img) > 0){
img <- 1-EBImage::channel(img, input$channel)
}
if(input$invert) {
img <- 1 - img
}
thr <- triangle(img, input$tri_offset)
signal <- EBImage::imageData(img) > thr
EBImage::imageData(img) <- (EBImage::imageData(img) - thr)*signal
shinyImageFile$Mean_Intensities[1,count1] <- mean(EBImage::imageData(img)[signal])
shinyImageFile$Median_Intensities[1,count1] <- median(EBImage::imageData(img)[signal])
plot(img)
title(paste0("Line ", count2))
}
})
}
else if(input$thresh == 4){
Background.Threshold <- numeric(input$bands)
output$plot3 <- renderPlot({
par(mfcol = c(1, input$bands))
count1 <- 0
Bands <- seq(1, 2*input$bands-1, by = 2)
count2 <- 0
for(j in Bands){
count1 <- count1 + 1
count2 <- count2 + 1
img <- seg.list[[i]][[j]]
if(colorMode(img) > 0){
img <- 1-EBImage::channel(img, input$channel)
}
if(input$invert) {
img <- 1 - img
}
Background.Threshold[count1] <- threshold_li(img)
signal <- EBImage::imageData(img) > Background.Threshold[count1]
EBImage::imageData(img) <- signal
plot(img)
title(paste0("Line ", count2))
}
shinyImageFile$Threshold <- Background.Threshold
})
shinyImageFile$Mean_Intensities <- matrix(0, nrow = 1, ncol = input$bands)
shinyImageFile$Median_Intensities <- matrix(0, nrow = 1, ncol = input$bands)
output$plot4 <- renderPlot({
par(mfcol = c(1, input$bands))
count1 <- 0
Bands <- seq(1, 2*input$bands-1, by = 2)
count2 <- 0
for(j in Bands){
count1 <- count1 + 1
count2 <- count2 + 1
img <- seg.list[[i]][[j]]
if(colorMode(img) > 0){
img <- 1-EBImage::channel(img, input$channel)
}
if(input$invert) {
img <- 1 - img
}
thr <- threshold_li(img)
signal <- EBImage::imageData(img) > thr
EBImage::imageData(img) <- (EBImage::imageData(img) - thr)*signal
shinyImageFile$Mean_Intensities[1,count1] <- mean(EBImage::imageData(img)[signal])
shinyImageFile$Median_Intensities[1,count1] <- median(EBImage::imageData(img)[signal])
plot(img)
title(paste0("Line ", count2))
}
})
}
})
})
observe({recursiveData()})
recursiveData <- eventReactive(input$data,{
isolate({
if (!is.null(shinyImageFile$Threshold)) {
AM <- shinyImageFile$Mean_Intensities
colnames(AM) <- paste0("Mean", 1:input$bands)
Med <- shinyImageFile$Median_Intensities
colnames(Med) <- paste0("Median", 1:input$bands)
if(input$thresh == 1){
BG.method <- matrix(c("Otsu", NA, NA), nrow = 1,
ncol = 3, byrow = TRUE)
colnames(BG.method) <- c("Background", "Offset", "Probability")
}
if(input$thresh == 2){
BG.method <- matrix(c("quantile", NA, input$quantile1),
nrow = 1, ncol = 3, byrow = TRUE)
colnames(BG.method) <- c("Background", "Offset", "Probability")
}
if(input$thresh == 3){
BG.method <- matrix(c("triangle", input$tri_offset, NA), nrow = 1,
ncol = 3, byrow = TRUE)
colnames(BG.method) <- c("Background", "Offset", "Probability")
}
if(input$thresh == 4){
BG.method <- matrix(c("Li", NA, NA), nrow = 1,
ncol = 3, byrow = TRUE)
colnames(BG.method) <- c("Background", "Offset", "Probability")
}
seg.list <- shinyImageFile$segmentation_list
img <- seg.list[[1]][[1]]
if(colorMode(img) > 0){
MODE <- input$channel
DF <- data.frame("File" = shinyImageFile$filename,
"Mode" = MODE,
"Strip" = input$selectStrip,
BG.method, AM, Med,
check.names = TRUE)
}else{
DF <- data.frame("File" = shinyImageFile$filename,
"Mode" = NA,
"Strip" = input$selectStrip,
BG.method, AM, Med,
check.names = TRUE)
}
if(inherits(try(IntensData, silent = TRUE), "try-error"))
IntensData <<- DF
else
IntensData <<- rbind(IntensData, DF)
output$intens <- renderDT({
DF <- IntensData
datatable(DF)
})
output$plot3 <- NULL
output$plot4 <- NULL
if(!is.null(shinyImageFile$Threshold))
shinyImageFile$Threshold <- NULL
if(!is.null(shinyImageFile$Mean_Intensities))
shinyImageFile$Mean_Intensities <- NULL
if(!is.null(shinyImageFile$Median_Intensities))
shinyImageFile$Median_Intensities <- NULL
# Save the workspace every time you add to intensity data
# save(shinyImageFile, IntensData,
# ExpInfo, MergedData, fit,
# modelPlot, LOB, LOD, LOQ,
# file=file.path(fs::path_home(), "Documents/LFApp/cal_autosave.RData"))
# showNotification("Workspace saved", duration=2, type="message")
}
})
})
observe({recursiveShowIntensData()})
recursiveShowIntensData <- eventReactive(input$showIntensData,{
isolate({
updateTabsetPanel(session, "tabs", selected = "tab3")
})
})
observe({recursiveDelete()})
recursiveDelete <- eventReactive(input$deleteData,{
isolate({
IntensData <<- NULL
output$intens <- renderDT({})
})
})
observe({recursiveDelete2()})
recursiveDelete2 <- eventReactive(input$deleteData2,{
isolate({
ExpInfo <<- NULL
MergedData <<- NULL
output$experiment <- renderDT({})
})
})
observe({recursiveDelete3()})
recursiveDelete3 <- eventReactive(input$deleteData3,{
isolate({
MergedData <<- NULL
CalibrationData <<- NULL
output$calibration <- renderDT({})
})
})
observe({recursiveRefresh()})
recursiveRefresh <- eventReactive(input$refreshData,{
isolate({
output$intens <- renderDT({
DF <- IntensData
datatable(DF)
})
})
})
observe({recursiveRefresh2()})
recursiveRefresh2 <- eventReactive(input$refreshData2,{
isolate({
output$experiment <- renderDT({
DF <- MergedData
datatable(DF)
})
})
})
observe({recursiveRefresh3()})
recursiveRefresh3 <- eventReactive(input$refreshData3,{
isolate({
output$calibration <- renderDT({
DF <- CalibrationData
datatable(DF)
})
})
})
observe({recursiveExpInfo()})
recursiveExpInfo <- eventReactive(input$expInfo,{
updateTabsetPanel(session, "tabs", selected = "tab4")
})
observe({recursiveUploadIntens()})
recursiveUploadIntens <- eventReactive(input$intensFile,{
isolate({
req(input$intensFile)
tryCatch(
DF <- read.csv(input$intensFile$datapath, header = TRUE,
check.names = TRUE),
error = function(e){stop(safeError(e))}
)
IntensData <<- DF
output$intens <- renderDT({
datatable(DF)
})
})
})
observe({recursiveUploadExpFile()})
recursiveUploadExpFile <- eventReactive(input$expFile,{
isolate({
req(input$expFile)
tryCatch(
DF <- read.csv(input$expFile$datapath, header = TRUE,
check.names = TRUE),
error = function(e){stop(safeError(e))}
)
ExpInfo <<- DF
MergedData <<- DF
suppressWarnings(rm(CalibrationData, pos = 1))
output$calibration <- renderDT({})
output$experiment <- renderDT({
datatable(DF)
})
})
})
observe({recursiveUploadPrepFile()})
recursiveUploadPrepFile <- eventReactive(input$prepFile,{
isolate({
req(input$prepFile)
tryCatch(
DF <- read.csv(input$prepFile$datapath, header = TRUE,
check.names = TRUE),
error = function(e){stop(safeError(e))}
)
CalibrationData <<- DF
MergedData <<- DF
output$calibration <- renderDT({
datatable(DF)
})
updateSelectInput(session = session, "concVar", choices = names(DF))
})
})
observe({recursiveMerge()})
recursiveMerge <- eventReactive(input$merge,{
isolate({
if (is.null(ExpInfo)) {
showNotification("Experiment info not found.", duration=3, type="error")
} else if (is.null(IntensData)) {
showNotification("Intensity data not found.", duration=3, type="error")
} else if (inherits(try(merge(ExpInfo, IntensData,
by.x = input$mergeExp,
by.y = input$mergeIntens, all = TRUE), silent = TRUE), "try-error")) {
showNotification("Error in the column IDs.", duration=5, type="error")
} else {
DF <- merge(ExpInfo, IntensData,
by.x = input$mergeExp,
by.y = input$mergeIntens, all = TRUE)
MergedData <<- DF
CalibrationData <<- DF
output$experiment <- renderDT({
datatable(DF)
})
}
})
})
observe({recursivePrepare()})
recursivePrepare <- eventReactive(input$prepare,{
DF <- MergedData
CalibrationData <<- DF
output$calibration <- renderDT({
datatable(DF)
})
updateSelectInput(session, "concVar", choices = names(DF))
updateTabsetPanel(session, "tabs", selected = "tab5")
})
observe({recursiveCombReps()})
recursiveCombReps <- eventReactive(input$combReps,{
isolate({
Cols <- c(grep("Mean", colnames(MergedData)),
grep("Median", colnames(MergedData)))
RES <- NULL
if(input$colorsBands > 1){
DF <- MergedData[,c(input$combRepsColSI, input$combRepsColCL)]
DFuni <- DF[!duplicated(DF),]
for (i in 1:nrow(DFuni)) {
sel <- DF[,1] == DFuni[i,1] & DF[,2] == DFuni[i,2]
tmp <- MergedData[sel, ]
tmp2 <- tmp[1, ]
if (input$radioReps == 1) #mean
tmp2[, Cols] <- colMeans(tmp[, Cols], na.rm = TRUE)
if (input$radioReps == 2) #median
tmp2[, Cols] <- apply(tmp[, Cols], 2, median, na.rm = TRUE)
RES <- rbind(RES, tmp2)
}
}else{
DF <- MergedData[,input$combRepsColSI]
for (spl in unique(MergedData[, input$combRepsColSI])) {
tmp <- MergedData[DF == spl, ]
tmp2 <- tmp[1, ]
if (input$radioReps == 1) #mean
tmp2[, Cols] <- colMeans(tmp[, Cols], na.rm = TRUE)
if (input$radioReps == 2) #median
tmp2[, Cols] <- apply(tmp[, Cols], 2, median, na.rm = TRUE)
RES <- rbind(RES, tmp2)
}
}
rownames(RES) <- 1:nrow(RES)
RES <- RES[order(RES[,input$combRepsColSI]),]
CalibrationData <<- RES
output$calibration <- renderDT({
datatable(RES)
})
})
})
observe({recursiveReshapeWide()})
recursiveReshapeWide <- eventReactive(input$reshapeWide,{
isolate({
rm.file <- (colnames(CalibrationData) != colnames(MergedData)[1] &
colnames(CalibrationData) != input$reshapeCol)
DF.split <- split(CalibrationData[,rm.file], CalibrationData[,input$reshapeCol])
N <- length(unique(CalibrationData[,input$reshapeCol]))
if(N > 1){
DF <- DF.split[[1]]
Cols <- c(grep("Mean", colnames(DF)),
grep("Median", colnames(DF)))
Cols <- c(Cols, which(colnames(DF) == input$combRepsColSI))
for(i in 2:N){
DF <- merge(DF, DF.split[[i]][,Cols], by = input$combRepsColSI,
suffixes = paste0(".", names(DF.split)[c(i-1,i)]))
}
CalibrationData <<- DF
}else{
DF <- CalibrationData
}
output$calibration <- renderDT({
datatable(DF)
})
})
})
MODELNUM <- 1
observe({recursiveRunCali()})
recursiveRunCali <- eventReactive(input$runCali,{
isolate({
# flush the output and plots
output$LOB <- renderText({})
output$LOD <- renderText({})
output$LOQ <- renderText({})
output$plot5 <- renderPlot({})
PATH.OUT <- input$folder
if (!file.exists(PATH.OUT)) dir.create(PATH.OUT)
concVar <- input$concVar
respVar <- paste0("(",input$respVar,")")
if(input$useLog){
if(input$chosenModel == 3){
k <- ceiling(length(unique(CalibrationData[,concVar]))/2)
FORMULA <- paste0(respVar, " ~ s(log10(", concVar, "), k = ", k, ")")
}else{
FORMULA <- paste0(respVar, " ~ log10(", concVar, ")")
}
}else{
if(input$chosenModel == 3){
k <- ceiling(length(unique(CalibrationData[,concVar]))/2)
FORMULA <- paste0(respVar, " ~ s(", concVar, ", k = ", k, ")")
}else{
FORMULA <- paste0(respVar, " ~ ", concVar)
}
}
if(input$chosenModel == 1 && !inherits(try(lm(as.formula(FORMULA), data=CalibrationData), silent = TRUE), "try-error")){
modelName <- "lm"
} else if(input$chosenModel == 2 && !inherits(try(loess(as.formula(FORMULA), data = CalibrationData), silent = TRUE), "try-error")){
modelName <- "loess"
} else if(input$chosenModel == 3 && !inherits(try(gam(as.formula(FORMULA), data = CalibrationData), silent = TRUE), "try-error")){
modelName <- "gam"
} else {
output$modelSummary <- renderPrint({print("Calibration can not be performed. Please check the formula.");
print(paste0("Formula: ",FORMULA))})
showNotification("Error in the formula!", duration = 5, type="error")
updateTabsetPanel(session, "tabs", selected = "tab6")
return(NULL)
}
info <- showNotification(paste("Fitting the model..."), duration = 0, type="message")
SUBSET <- input$subset
FILENAME <<- paste0(format(Sys.time(), "%Y%m%d_%H%M%S_"), input$analysisName)
header <- c('---',
'title: "Calibration Analysis"',
'date: "`r format(Sys.time(), \'%d %B %Y\')`"',
'output:',
' rmarkdown::html_document:',
' theme: united',
' highlight: tango',
' toc: true',
' number_sections: true',
'params:',
paste0(' filename: ', file.path(PATH.OUT, FILENAME)),
paste0(' formula: ', FORMULA),
'---')
save(CalibrationData, FORMULA, SUBSET, PATH.OUT,
file = file.path(PATH.OUT, paste0(FILENAME, "_Data.RData")))
if (input$chosenModel == 1) {
template <- readLines(system.file("markdown", "CalibrationAnalysis(lm).Rmd",
package = "LFApp"))
write(header, file=file.path(PATH.OUT, paste0(FILENAME, "_Analysis.Rmd")), append=FALSE)
write(template, file=file.path(PATH.OUT, paste0(FILENAME, "_Analysis.Rmd")), append=TRUE)
} else if (input$chosenModel == 2) {
template <- readLines(system.file("markdown", "CalibrationAnalysis(loess)).Rmd",
package = "LFApp"))
write(header, file=file.path(PATH.OUT, paste0(FILENAME, "_Analysis.Rmd")), append=FALSE)
write(template, file=file.path(PATH.OUT, paste0(FILENAME, "_Analysis.Rmd")), append=TRUE)
} else if (input$chosenModel == 3) {
template <- readLines(system.file("markdown", "CalibrationAnalysis(gam).Rmd",
package = "LFApp"))
write(header, file=file.path(PATH.OUT, paste0(FILENAME, "_Analysis.Rmd")), append=FALSE)
write(template, file=file.path(PATH.OUT, paste0(FILENAME, "_Analysis.Rmd")), append=TRUE)
}
rmarkdown::render(input = file.path(PATH.OUT, paste0(FILENAME, "_Analysis.Rmd")),
output_file = file.path(PATH.OUT, paste0(FILENAME, "_Analysis.html")))
output$modelSummary <- renderPrint({ fit })
output$plot5 <- renderPlot({
modelPlot
})
output$LOB <- renderText({
paste0("Limit of Blank (LOB): ", signif(LOB, 3))
})
output$LOD <- renderText({
paste0("Limit of Detection (LOD): ", signif(LOD, 3))
})
output$LOQ <- renderText({
paste0("Limit of Quantification (LOQ): ", signif(LOQ, 3))
})
# Adding the analysis name and model formula to the table
modelName <- rep(modelName, nrow(CalibrationData))
modelFormula <- rep(FORMULA, nrow(CalibrationData))
modelDF <- cbind(modelName, modelFormula, predFunc(CalibrationData))
colnames(modelDF) <- c(paste0(input$analysisName, ".model"),
paste0(input$analysisName, ".formula"),
paste0(input$analysisName, ".", input$concVar, ".fit"))
if(SUBSET != ""){
subsetIndex <- function (x, subset){
e <- substitute(subset)
r <- eval(e, x, parent.frame())
r & !is.na(r)
}
Index <- eval(call("subsetIndex", x = CalibrationData,
subset = parse(text = SUBSET)))
modelDF[!Index,] <- NA
}
DF <- cbind(CalibrationData, modelDF)
CalibrationData <<- DF
output$calibration <- renderDT({
datatable(DF)
})
MODELNUM <<- MODELNUM + 1
updateTextInput(session=session, inputId="analysisName", value=paste0("Model", MODELNUM))
removeNotification(info)
updateTabsetPanel(session, "tabs", selected = "tab6")
})
})
observe(resetFolder())
resetFolder <- eventReactive(input$folder,{
isolate({
if(substring(input$folder,1,nchar(file.path(fs::path_home()))) != file.path(fs::path_home()))
updateTextInput(session=session, inputId = "folder", value = file.path(fs::path_home()))
})
})
observe({recursiveOpenReport()})
recursiveOpenReport <- eventReactive(input$openReport,{
isolate({
browseURL(file.path(input$folder, paste0(FILENAME, "_Analysis.html")),
browser = getOption("browser"))
})
})
#creates the textbox below plot2 about the plot_brush details and etc
output$thresh <- renderText({
if(!is.null(shinyImageFile$Threshold))
paste0("Threshold(s): ", paste0(signif(shinyImageFile$Threshold, 4), collapse = ", "))
})
output$meanIntens <- renderText({
if(!is.null(shinyImageFile$Threshold))
paste0("Mean intensities: ", paste0(signif(shinyImageFile$Mean_Intensities, 4), collapse = ", "))
})
output$medianIntens <- renderText({
if(!is.null(shinyImageFile$Threshold))
paste0("Median intensities: ", paste0(signif(shinyImageFile$Median_Intensities, 4), collapse = ", "))
})
output$intens <- renderDT({
DF <- IntensData
datatable(DF)
})
output$folder <- renderPrint({
paste0("Folder for Results: ", parseDirPath(c(wd=fs::path_home()), input$folder))
})
#allows user to download data
output$downloadData <- downloadHandler(
filename = "IntensityData.csv",
content = function(file) {
write.csv(IntensData, file, row.names = FALSE)
}
)
output$downloadData2 <- downloadHandler(
filename = "MergedData.csv",
content = function(file) {
write.csv(MergedData, file, row.names = FALSE)
}
)
output$downloadData3 <- downloadHandler(
filename = "CalibrationData.csv",
content = function(file) {
write.csv(CalibrationData, file, row.names = FALSE)
}
)
#When user clicks the return to command line button
#stops the shiny app
# prevents user from quitting shiny using ^C on commandline
observe({recursiveStop()})
recursiveStop <- eventReactive(input$stop,{
isolate({
suppressWarnings(rm(IntensData, pos = 1))
suppressWarnings(rm(ExpInfo, pos = 1))
suppressWarnings(rm(MergedData, pos = 1))
suppressWarnings(rm(CalibrationData, pos = 1))
stopApp()
})
})
# Checking if workspace file exist
observe({
if (file.exists(file.path(fs::path_home(), "Documents/LFApp/cal_autosave.RData"))) {
showModal(modalDialog(
title = "Old workspace backup found",
"Do you want to restore previous workspace?",
h6("If you do not restore the old workspace, it will be overwritten!"),
footer = tagList(
actionButton("no_restore", "No"),
actionButton("restore_work", "Yes")
)
))
} else {
startAutosave(TRUE)
}
})
observeEvent(input$no_restore, {
startAutosave(TRUE)
removeModal()
})
observeEvent(input$restore_work, {
load(file=file.path(fs::path_home(), "Documents/LFApp/cal_autosave.RData"))
# Loading the variables properly. Without this the variables are loaded in the observe scope only
shinyImageFile <<- shinyImageFile
IntensData <<- IntensData
ExpInfo <<- ExpInfo
MergedData <<- MergedData
fit <<- fit
modelPlot <<- modelPlot
LOB <<- LOB
LOD <<- LOD
LOQ <<- LOQ
# Loading the image on the first plot
if (!is.null(shinyImageFile$shiny_img_final))
output$plot1 <- renderPlot({EBImage::display(shinyImageFile$shiny_img_final, method = "raster")})
# Loading datatables
output$intens <- renderDT(datatable(IntensData))
output$experiment <- renderDT(datatable(ExpInfo))
output$calibration <- renderDT(datatable(MergedData))
# Loading model in results tab
if (!is.null(fit) && !is.null(LOB) && !is.null(LOD) && !is.null(LOQ)) {
output$modelSummary <- renderPrint({ fit })
output$plot5 <- renderPlot({ modelPlot })
output$LOB <- renderText({ paste0("Limit of Blank (LOB): ", signif(LOB, 3)) })
output$LOD <- renderText({ paste0("Limit of Detection (LOD): ", signif(LOD, 3)) })
output$LOQ <- renderText({ paste0("Limit of Quantification (LOQ): ", signif(LOQ, 3)) })
}
startAutosave(TRUE)
removeModal()
})
# Autosaving every minute
observe({
if (startAutosave()) {
invalidateLater(300000, session)
if (!file.exists(file.path(fs::path_home(), "Documents/LFApp"))) dir.create(file.path(fs::path_home(), "Documents/LFApp"))
save(shinyImageFile, IntensData,
ExpInfo, MergedData, fit,
modelPlot, LOB, LOD, LOQ,
file=file.path(fs::path_home(), "Documents/LFApp/cal_autosave.RData"))
showNotification("Workspace saved", duration=2, type="message")
}
})
# A function to remove the autosave file if the app was closed properly
# onStop(function() file.remove(file.path(fs::path_home(), "Documents/LFApp/cal_autosave.RData")))
}
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