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server.R
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library("shiny")
library("reshape2")
library("plotly")
library("ggplot2")
library("plyr")
library("XLConnectJars")
library("XLConnect")
library("xlsx")
library("xlsxjars")
options(shiny.sanitize.errors = FALSE)
pdf(NULL)
function(input,output,session){
# cbind.fill <- function(...){
# nm <- list(...)
# nm <- lapply(nm, as.matrix)
# n <- max(sapply(nm, nrow))
# do.call(cbind, lapply(nm, function (x) rbind(x, matrix(, n-nrow(x), ncol(x)))))
# }
output$data_notice <- renderText("Choose a valid .xls(x) data file")
output$meta_notice <- renderText("Download, complete and upload a metadata file")
output$respiration_notice <- renderText("Please ensure valid Q2 data, Q2 metadata and experimental conditions are loaded")
# well_cols <- c("A","B","C","D","E","F")
#
# wells <- NULL
# for(i in 1:8){
# for(j in well_cols){
# wells <- c(wells,paste0(j,i))
# }
# }
#This loads the Q2_Data file and stores it within the Q2_data() variable
Q2_data <- reactive({
if (!is.null(input$xlsInput)){
plate_data <- readWorksheetFromFile(input$xlsInput$datapath,sheet=1,header=FALSE)
if (plate_data[1,1] != "Q2 RUN informaton"){
output$data_notice <- renderText("Does not appear to be a Q2 data file")
# plate_data <- NULL
return(plate_data)
} else {
tryCatch({
x <- as.POSIXct(plate_data[23,4],format="%m/%d/%Y %H:%M:%S")},
warning = function(w) {},
error = function(e) {
print(e)
})
if (is.na(x)){
interval <- as.integer(as.POSIXct(plate_data[24,4],format="%d/%m/%Y %H:%M:%S") - as.POSIXct(plate_data[23,4],format="%d/%m/%Y %H:%M:%S"))
}else{
interval <- as.integer(as.POSIXct(plate_data[24,4],format="%m/%d/%Y %H:%M:%S") - as.POSIXct(plate_data[23,4],format="%m/%d/%Y %H:%M:%S"))
}
plate_data <- plate_data[-(1:21),]
names(plate_data) <- plate_data[1,]
plate_data <- plate_data[-1,]
for(X in 0:(length(plate_data$HRS)-1)) {
plate_data$HRS[[X+1]] <- formatC(X*interval, width=3, flag="0")
}
plate_data$HRS <- as.integer(plate_data$HRS)
colnames(plate_data)[which(names(plate_data) == "HRS")] <- paste("MINS")
output$data_notice <- renderText("Q2 data file appears to be valid")
#print(plate_data[,colSums(is.na(plate_data))==0])
#return(plate_data)
return(plate_data[,colSums(is.na(plate_data))==0])
}
}
})
output$downloadTemplate <- downloadHandler(
filename = function() {
"Q2_metadata_template_48_wells.xlsx"
},
content = function(file) {
myfile <- srcpath <- "./resources/Q2_metadata_template_48_wells.xlsx"
file.copy(myfile, file)
}
)
Q2_plate_metadata <- reactive({
if (!is.null(input$metadata)){
plate_metadata <- readWorksheetFromFile(input$metadata$datapath,sheet=1,header=TRUE)
if (("Well" %in% colnames(plate_metadata)) && ("Plate" %in% colnames(plate_metadata))){
output$meta_notice <- renderText("Q2 metadata file appears to be valid")
#df2[df2$W %in% colnames(test_data2[1:length(test_data2)]),]
#print(plate_metadata[plate_metadata$Well %in% colnames(Q2_data()[7:length(Q2_data())]),])
#return(plate_metadata)
#print(na.omit(plate_metadata, cols=c(Sample.Name,Area,Fresh_Weight,Dry_Weight)))
return(plate_metadata[!is.na(plate_metadata$Sample.Name) & !is.na(plate_metadata$Area) & !is.na(plate_metadata$Fresh_Weight) & !is.na(plate_metadata$Dry_Weight),])
#return(plate_metadata[plate_metadata$Well %in% colnames(Q2_data()[7:length(Q2_data())]),])
#return(plate_metadata[intersect(plate_metadata$Well,colnames(Q2_data()[7:length(Q2_data())])),])
} else {
output$meta_notice <- renderText("Does not appear to be a valid metadata file")
return(plate_metadata)
}
}
})
mismatched_wells <- reactive({
req(Q2_data())
req(Q2_plate_metadata())
mismatched <- setdiff(colnames(Q2_data()[-(1:6)]),Q2_plate_metadata()$Well)
return(mismatched)
})
observe({
if (!is.null(mismatched_wells())){
# print(colnames(Q2_data()[-(1:6)]))
#
# print(Q2_plate_metadata()$Well)
# mismatched <- setdiff(colnames(Q2_data()[-(1:6)]),Q2_plate_metadata()$Well)
if (identical(mismatched_wells(),character(0))){
output$catch_notice <- renderText(paste(""))
} else {
output$catch_notice <- renderText(paste("The following wells don't match between the data and metadata files:", paste(mismatched_wells(), collapse=" ")))
}
}
})
observeEvent({input$tabs == "Q2_fluoro_tab"},
if (is.null(input$xlsInput) || (is.null(Q2_data())) || (colnames(Q2_data()[1]) != "ID")){
output$fluoro_notice <- renderText("Please ensure a valid Q2 data file is loaded")
} else if (colnames(Q2_data()[1]) == "ID"){
output$fluoro_notice <- renderText("")
output$fluoro <- renderPlotly(
if (!is.null(input$xlsInput)){
melting <- Q2_data()
#PING#
# for (Q in Q2_blanks()){
# melting[[Q]] <- NULL
# }
#PING#
#Replace this with another setdiff function that takes the number of wells in the data file and the number of wells in the metadata
#and checks to make sure they're the same, dropping blanks.
#Turn this into its own check/function that checks the metadata and data BEFORE proceeding
#Existing:
# wells_and_blanks <- setdiff(wells, Q2_blanks())
# melting <- melt(melting, measure.vars = wells_and_blanks)
# melting$value <- as.numeric(melting$value)
#Unsure about what this does... but used in the fluoro plot (comment out to see what happens)
melting <- melt(melting, measure.vars = colnames(Q2_data()[-(1:6)]))
melting$value <- as.numeric(melting$value)
fluoro_plot <- ggplot(melting, aes(x=MINS, y=value, group=variable, color=variable)) + geom_line()
fluoro_plot <- fluoro_plot + labs(x = "Time (min)", y = "Q2 Fluorescence", title = "Q2 Flourescence over Time", color = "Well")
fluoro_plot <- fluoro_plot + scale_y_continuous(limits = c(-0.2, 1.2), breaks = seq(-0.2,1.2,by=0.2), expand=c(0,0))
fluoro_plot <- fluoro_plot + scale_x_continuous(limits = c(min(Q2_data()$MINS, na.rm = TRUE),max(Q2_data()$MINS, na.rm = TRUE)), breaks = seq(min(Q2_data()$MINS, na.rm = TRUE),max(Q2_data()$MINS, na.rm = TRUE),by=100), expand=c(0,0))
fluoro_plot <- fluoro_plot + theme(axis.text.x = element_text(hjust = 1))
fluoro_plot <- fluoro_plot + theme(axis.title.x = element_text(vjust = -0.5))
}
)
if (is.null(input$UI_time_start) && is.null(input$UI_time_stop)){
output$fluoro_start_spot <- renderUI(numericInput("UI_time_start",
"Start Time",
as.numeric(paste0(min(Q2_data()$MINS, na.rm = TRUE))),
min=as.numeric(paste0(min(Q2_data()$MINS, na.rm = TRUE))),
max=as.numeric(paste0(max(Q2_data()$MINS, na.rm = TRUE))),
step=Q2_data()$MINS[2]))
output$fluoro_end_spot <- renderUI(numericInput("UI_time_stop",
"End Time",
value=as.numeric(paste0(max(Q2_data()$MINS, na.rm = TRUE))),
min=as.numeric(paste0(min(Q2_data()$MINS, na.rm = TRUE))),
max=as.numeric(paste0(max(Q2_data()$MINS, na.rm = TRUE))),
step=Q2_data()$MINS[2]))
}
}
)
observe({
if (!is.null(input$UI_time_start) || (!is.null(input$UI_time_stop))){
if (!is.na(as.numeric(input$UI_time_start)) && !is.na(as.numeric(input$UI_time_stop))){
if (as.numeric(input$UI_time_start) > -1 || as.numeric(input$UI_time_stop) > -1) {
if (as.numeric(input$UI_time_stop) - as.numeric(input$UI_time_start) > 0){
if (as.numeric(input$UI_time_start) < as.numeric(paste0(min(Q2_data()$MINS, na.rm = TRUE))) || as.numeric(input$UI_time_stop) > as.numeric(paste0(max(Q2_data()$MINS, na.rm = TRUE)))){
output$fluro_duration <- renderText(paste("Ensure start time is equal to or greater than ", paste0(min(Q2_data()$MINS, na.rm = TRUE)), " and end time is equal to or less than ",paste0(max(Q2_data()$MINS, na.rm = TRUE))))
}
else{
multiplier <- as.numeric(Q2_data()$MINS[2])
if (as.numeric(input$UI_time_start) %% multiplier != 0 || as.numeric(input$UI_time_stop) %% multiplier != 0){
output$fluro_duration <- renderText(paste("Ensure start and stop times are a multiple of ", multiplier))
}
else
{
output$fluro_duration <- renderText(paste("Duration: ",as.numeric(input$UI_time_stop) - as.numeric(input$UI_time_start)," minutes"))
}
}
}
else{
output$fluro_duration <- renderText(paste("Ensure start time is before end time"))
}
}
else{
output$fluro_duration <- renderText(paste("Ensure start and end times are positive"))
}
}
else{
output$fluro_duration <- renderText(paste("Please ensure the start and end times are numbers"))
}
}
})
observe({
if (input$is_MSLP){
updateTextInput(session,"altitude",value = paste(""), label = paste("Altitude not required"))
shinyjs::disable("altitude")
}
else{
updateTextInput(session,"altitude", label = paste("Altitude (m)"))
shinyjs::enable("altitude")
}
})
#PING#
# Q2_blanks <- reactive({
#
# blanks <- vector()
#
# if (!is.null(Q2_data()) && ((colnames(Q2_data()[1]) == "ID") && (colnames(Q2_data()[6]) == "TEMPERATURE"))){
#
# for (i in 7:54){
#
# print(Q2_data()[1,i])
#
# if (is.na(Q2_data()[,i])){
#
# blanks <- c(blanks,colnames(Q2_data()[i]))
#
# }
# }
# }
#
# return(blanks)
#
# })
#
Q2_slopes <- reactive({
req(input$UI_time_start)
req(input$UI_time_stop)
Q2_subset <- subset(Q2_data(),Q2_data()$MINS >= input$UI_time_start & Q2_data()$MINS <= input$UI_time_stop)
#PING#
#See previous ping.
# wells_and_blanks <- setdiff(wells, Q2_blanks())
#
# Q2_subset_temp <- Q2_subset[,7:54]
# Q2_subset_temp <- Q2_subset_temp[,wells_and_blanks]
# Q2_subset[,7:54] <- Q2_subset_temp
#
# for (Q in Q2_blanks()){
# Q2_subset[[Q]] <- NULL
# }
# Q2_subset_temp <- Q2_subset[,7:54]
# Q2_subset_temp <- Q2_subset_temp[,wells_and_blanks]
# Q2_subset[,7:54] <- Q2_subset_temp
#Q2_subset <- Q2_subset[-(1:6)]
slopes <- NULL
#PING#
#This should only proceed when we have confirmed that there are no missing fields
#Proceed based on the data fucntion and wells present
#for (Y in wells_and_blanks){
for (Y in colnames(Q2_subset[-(1:6)])){
holder <- lm(Q2_subset[[paste(Y,sep="")]] ~ Q2_subset$MINS)
#PING#
slopes[[paste(Y,sep="")]] <- holder$coefficients[[2]]
}
slopes <- cbind(colnames(Q2_subset[-(1:6)]), slopes)
slopes[,2] <- as.numeric(slopes[,2])*60
return(slopes)
})
Q2_Respiration <- reactive({
req(as.numeric(input$UI_time_start))
req(as.numeric(input$UI_time_stop))
req(identical(mismatched_wells(),character(0)))
#PING#
#req(identical(mismatched_wells(),character(0)))
temp_Q2_plate_metadata <- NULL
meta <- GoodMeta()
metafile <- input$metadata
altitude <- as.numeric(input$altitude)
sitePressure <- as.numeric(input$sitePressure)
tubeVol <- as.numeric(input$tubeVol)
temperature <- as.numeric(input$temperature)
#NB: One atmosphere of pressure is 101.5 kPa, so the pressure should be a similar value to this
if (input$is_MSLP){
pressureCalc <- sitePressure
}
else{
pressureCalc <- sitePressure-(101.35*(1-(1-(altitude/44307.69231))^5.25328))
}
if (!is.null(input$xlsInput) &&
(!is.na(as.numeric(input$UI_time_start) || (!is.na(as.numeric(input$UI_time_stop))))) &&
(as.numeric(input$UI_time_start) < as.numeric(input$UI_time_stop)) && (meta == "0") &&
(!is.null(mean(c(as.numeric(Q2_slopes()[3:4,2])))))){
#AFB- replace airSlope method with data selection method in future
airSlope <- mean(c(as.numeric(Q2_slopes()[3:4,2])))
temp_Q2_slopes <- Q2_slopes()[,2]
temp_Q2_plate_metadata <- Q2_plate_metadata()
temp_Q2_slopes <- lapply(temp_Q2_slopes, as.character)
temp_Q2_slopes <- as.numeric(temp_Q2_slopes)
# temp_Q2_plate_metadata$Slopes <- as.numeric(Q2_slopes()[,2])
temp_Q2_plate_metadata$Slopes <- as.numeric(temp_Q2_slopes)
temp_Q2_plate_metadata$Area <- as.numeric(temp_Q2_plate_metadata$Area)
temp_Q2_plate_metadata$Fresh_Weight <- as.numeric(temp_Q2_plate_metadata$Fresh_Weight)
temp_Q2_plate_metadata$Dry_Weight <- as.numeric(temp_Q2_plate_metadata$Dry_Weight)
# temp_Q2_plate_metadata[,4] <- sapply(temp_Q2_plate_metadata[,4], as.numeric)
# temp_Q2_plate_metadata[,5] <- sapply(temp_Q2_plate_metadata[,5], as.numeric)
# temp_Q2_plate_metadata[,6] <- sapply(temp_Q2_plate_metadata[,6], as.numeric)
# temp_Q2_plate_metadata[,4] <- as.numeric(temp_Q2_plate_metadata[,4])
# temp_Q2_plate_metadata[,5] <- as.numeric(temp_Q2_plate_metadata[,5])
# temp_Q2_plate_metadata[,6] <- as.numeric(temp_Q2_plate_metadata[,6])
# temp_Q2_plate_metadata$Area_Resp <- -(pressureCalc*((20.95/100)*tubeVol*(temp_Q2_slopes))/(8314*(273.15+temperature))/(60*60)*1000000*(10000/temp_Q2_plate_metadata$Area))
# temp_Q2_plate_metadata$Fresh_Resp <- -(pressureCalc*((20.95/100)*tubeVol*(temp_Q2_slopes))/(8314*(273.15+temperature))/(60*60)*1000000*(1/temp_Q2_plate_metadata$Fresh_Weight)*1000)
# temp_Q2_plate_metadata$Dry_Resp <- -(pressureCalc*((20.95/100)*tubeVol*(temp_Q2_slopes))/(8314*(273.15+temperature))/(60*60)*1000000*(1/temp_Q2_plate_metadata$Dry_Weight)*1000)
temp_Q2_plate_metadata$Area_Resp <- -(pressureCalc*((20.95/100)*tubeVol*(temp_Q2_slopes))/(8314*(273.15+temperature))/(60*60)*1000000*(10000/temp_Q2_plate_metadata[,4]))
temp_Q2_plate_metadata$Fresh_Resp <- -(pressureCalc*((20.95/100)*tubeVol*(temp_Q2_slopes))/(8314*(273.15+temperature))/(60*60)*1000000*(1/temp_Q2_plate_metadata[,5])*1000)
temp_Q2_plate_metadata$Dry_Resp <- -(pressureCalc*((20.95/100)*tubeVol*(temp_Q2_slopes))/(8314*(273.15+temperature))/(60*60)*1000000*(1/temp_Q2_plate_metadata[,6])*1000)
#PING#
#temp_Q2_plate_metadata <- subset(temp_Q2_plate_metadata, !(temp_Q2_plate_metadata$Well %in% Q2_blanks()))
#Q2_plate_metadata()$Well
temp_Q2_plate_metadata$Well <- factor(temp_Q2_plate_metadata$Well, levels = temp_Q2_plate_metadata$Well)
#print(str(temp_Q2_plate_metadata))
return(temp_Q2_plate_metadata)
}
else if (!is.na(as.numeric(input$UI_time_start) || (!is.na(as.numeric(input$UI_time_stop))))){
temp_Q2_plate_metadata <- data.frame("")
return(temp_Q2_plate_metadata)
}
})
observe({
req(GoodMeta() == 0)
req(Q2_metadata_table())
if (!is.na(as.numeric(input$UI_time_start) || (!is.na(as.numeric(input$UI_time_stop))))){
output$respiration <- renderTable(digits = 4,Q2_Respiration()[,-1])
output$Resp_Meta <- renderTable(Q2_metadata_table(), colnames = FALSE)
}
})
Q2_metadata_table <- reactive({
req(GoodMeta())
if ((!is.null(Q2_Respiration())) && (!is.na(as.numeric(input$UI_time_start) || (!is.na(as.numeric(input$UI_time_stop)))))){
metadata_table <- data.frame(matrix(NA,nrow=0, ncol=2))
if (GoodMeta() == 0){
if (input$is_MSLP){
metadata_table <-rbind(metadata_table, data.frame(X1="Altitude (m)", X2="Pressure already MSL"))
}
else{
metadata_table <-rbind(metadata_table, data.frame(X1="Altitude (m)", X2=input$altitude))
}
metadata_table <- rbind(metadata_table, data.frame(X1="Pressure (kpa)", X2=input$sitePressure))
metadata_table <- rbind(metadata_table, data.frame(X1="Tube Vol (mL)", X2=input$tubeVol))
metadata_table <- rbind(metadata_table, data.frame(X1="Temperature (C)", X2=input$temperature))
metadata_table <- rbind(metadata_table, data.frame(X1="Start Time (min)", X2=as.character(input$UI_time_start)))
metadata_table <- rbind(metadata_table, data.frame(X1="Stop Time (min)", X2=as.character(input$UI_time_stop)))
metadata_table <- rbind(metadata_table, data.frame(X1="Q2 Data File", X2=input$xlsInput$name))
metadata_table <- rbind(metadata_table, data.frame(X1="Metadata File", X2=input$metadata$name))
}
return(metadata_table)
}
})
observe({
req(as.numeric(input$UI_time_start))
req(as.numeric(input$UI_time_stop))
req(GoodMeta() == 0)
#AFB - removing selection [(-1:4),] to restore all rows to the charting, remove standards with complete cases method.
if ((!is.null(Q2_Respiration())) && (!is.na(as.numeric(input$UI_time_start) || (!is.na(as.numeric(input$UI_time_stop)))))){
output$Resp_Area <- renderPlotly({
#resp_area_plot <- ggplot(Q2_Respiration()[-(1:4),], aes(x=Well, y=Area_Resp)) + geom_bar(stat="identity")
resp_area_plot <- ggplot(Q2_Respiration(), aes(x=Well, y=Area_Resp)) + geom_bar(stat="identity")
#resp_area_plot <- ggplot(Q2_Respiration()[complete.cases(Q2_Respiration()$Area_Resp),],
# aes(x=Well, y=Area_Resp)) + geom_bar(stat="identity")
resp_area_plot <- resp_area_plot + labs(x = "", y = paste0("\u03BC","mol Oxygen /m*m/s"), title = "Respiration based on Leaf Area")
resp_area_plot <- resp_area_plot + scale_y_continuous(expand=c(0,0))
# resp_area_plot <- resp_area_plot + theme_bw() + theme(axis.title.x = element_text(vjust = 1),axis.title.y = element_text(hjust = -1),axis.text.x = element_text(angle = 90, size=8))
resp_area_plot <- resp_area_plot + theme_bw() + theme(axis.text.x = element_text(angle = 90, size=8, vjust = 1))
resp_area_plot
})
}
})
observe({
req(as.numeric(input$UI_time_start))
req(as.numeric(input$UI_time_stop))
req(GoodMeta() == 0)
if ((!is.null(Q2_Respiration())) && (!is.na(as.numeric(input$UI_time_start) || (!is.na(as.numeric(input$UI_time_stop)))))){
output$Resp_Fresh_Mass <- renderPlotly({
#resp_area_plot <- ggplot(Q2_Respiration()[-(1:4),], aes(x=Well, y=Fresh_Resp)) + geom_bar(stat="identity")
#resp_area_plot <- ggplot(Q2_Respiration()[complete.cases(Q2_Respiration()$Fresh_Resp),],
#aes(x=Well, y=Fresh_Resp)) + geom_bar(stat="identity")
resp_area_plot <- ggplot(Q2_Respiration(), aes(x=Well, y=Fresh_Resp)) + geom_bar(stat="identity")
resp_area_plot <- resp_area_plot + labs(x = "", y = paste0("nmol Oxygen /g/s"), title = "Respiration based on Leaf Mass (Fresh)")
resp_area_plot <- resp_area_plot + scale_y_continuous(expand=c(0,0))
resp_area_plot <- resp_area_plot + theme_bw() + theme(axis.title.x = element_text(vjust = -0.5),axis.title.y = element_text(hjust = -1),axis.text.x = element_text(angle = 90, size=8))
resp_area_plot
})
}
})
observe({
req(as.numeric(input$UI_time_start))
req(as.numeric(input$UI_time_stop))
req(GoodMeta() == 0)
if ((!is.null(Q2_Respiration())) && (!is.na(as.numeric(input$UI_time_start) || (!is.na(as.numeric(input$UI_time_stop)))))){
output$Resp_Dry_Mass <- renderPlotly({
# resp_area_plot <- ggplot(Q2_Respiration()[-(1:4),], aes(x=Well, y=Dry_Resp)) + geom_bar(stat="identity")
#resp_area_plot <- ggplot(Q2_Respiration()[complete.cases(Q2_Respiration()$Dry_Resp),], aes(x=Well, y=Dry_Resp)) + geom_bar(stat="identity")
resp_area_plot <- ggplot(Q2_Respiration(), aes(x=Well, y=Dry_Resp)) + geom_bar(stat="identity")
resp_area_plot <- resp_area_plot + labs(x = paste0(c("\n")), y = paste0("nmol Oxygen /g/s"), title = "Respiration based on Leaf Mass (Dry)")
resp_area_plot <- resp_area_plot + scale_y_continuous(expand=c(0,0))
resp_area_plot <- resp_area_plot + theme_bw() + theme(axis.title.x = element_text(vjust = -0.5),axis.title.y = element_text(hjust = -1),axis.text.x = element_text(angle = 90, size=8))
resp_area_plot
})
}
})
output$data_download <- renderUI(
if (!is.null(Q2_Respiration()) && (!is.null(input$UI_time_start) || (!is.null(input$UI_time_stop)))){
downloadButton("downloadBtn", "Download Respiration Data")
}
)
# xlsOutput <- reactive({
# return(Q2_Respiration())
# print(Q2_Respiration())
# })
output$downloadBtn <- downloadHandler(
filename = function() {paste((strsplit(input$xlsInput$name, "\\.")[[1]][1]),"_respiration.xlsx")},
# content = function(file) {write.csv(rbind.fill(Q2_Respiration(),Q2_metadata_table()), file, row.names=FALSE)}
# content = function(file) {write.xlsx(rbind.fill(Q2_Respiration(),Q2_metadata_table()), file, row.names=FALSE)}
# content = function(file) {write.xlsx(xlsOutput(), file, row.names = FALSE)}
content = function(file) {saveWorkbook(xlsOutput(), file)}
#content = function(file) {write.csv(Q2_Respiration(), file, row.names = FALSE)}
#print(Q2_Respiration())
)
xlsOutput <- reactive({
req(GoodMeta() == 0)
xlsoutput <- createWorkbook()
xlsRespiration <- xlsx::createSheet(wb=xlsoutput, sheetName=paste("Respiration"))
xlsMetadata <- xlsx::createSheet(wb=xlsoutput, sheetName=paste("Metadata"))
addDataFrame(x=Q2_Respiration(), sheet=xlsRespiration, row.names = FALSE)
addDataFrame(x=Q2_metadata_table(), sheet=xlsMetadata, row.names = FALSE, col.names = FALSE)
return(xlsoutput)
})
GoodMeta <- reactive({
stuff <- NULL
metafile <- input$metadata
altitude <- input$altitude
pressure <- input$sitePressure
tubeVol <- input$tubeVol
temperature <- input$temperature
if (is.null(metafile)){
stuff <- c(stuff,"metadata file")
}
if (((altitude == "") || (is.na(as.numeric(altitude)*1))) && !input$is_MSLP){
stuff <- c(stuff,"altitude")
}
if ((pressure == "") || (is.na(as.numeric(pressure)*1))){
stuff <- c(stuff,"pressure")
}
if ((tubeVol == "") || (is.na(as.numeric(tubeVol)*1))){
stuff <- c(stuff,"tube volume")
}
if ((temperature == "") || (is.na(as.numeric(temperature)*1))){
stuff <- c(stuff,"temperature")
}
if (!(identical(mismatched_wells(),character(0)))){
stuff <- c(stuff,"mismatched wells")
}
if (is.null(input$UI_time_start) || (is.null(input$UI_time_stop))){
if (!is.numeric(input$UI_time_start) || (!is.numeric(input$UI_time_stop))){
stuff <- c(stuff, "respiration times")
}
}
if (!is.null(stuff)){
output$respiration_notice <- renderText(c(print("Please check the following metadata: "),paste(stuff,collapse=", ")))
return("1")
} else if (length(setdiff(colnames(Q2_data()[7:length(Q2_data())]), Q2_plate_metadata()$Well)) != 0) {
print("Weee!")
return("1")
} else {
output$respiration_notice <- renderText("")
return("0")
}
})
#PING#
#List blanks in here and in Metadata loading table
# output$data_blanks <- renderText({
#
# if (length(Q2_blanks()) != 0){
#
# c(print("The following wells have been identified as blank: "),paste(Q2_blanks(),collapse=", "))
#
# }
#
# else{NULL}
#
# })
output$Q2_Data <- renderTable({
Q2_data()
})
#PING#
#Put some stuff in here and make sure that it lists the number of missing wells/plates BEFORE running
output$Q2_Meta <- renderTable(
Q2_plate_metadata()
)
session$onSessionEnded(function() {
dev.off(which = dev.cur())
# stopApp()
# q("no")
})
}