Nothing
normalizeByBiomass <-
function (inputData, biomass, save = TRUE, folder, output = "norm_bio")
{
## Function to check if file is CSV ##
isCSVdlg <- function(titleMSG, errorMSG) {
t = 0
while (t == 0) {
checkIfCsv <- dlgOpen(title = titleMSG, multiple = FALSE)$res
checkIfCsv2 <- basename(checkIfCsv)
checkIfCsv3 <- unlist(strsplit(checkIfCsv2, "\\."))
checkIfCsv4 <- checkIfCsv3[length(checkIfCsv3)]
if (checkIfCsv4 %in% c("CSV", "csv")) {
t = 1
return(checkIfCsv)
} else {
dlgMessage(errorMSG)
}
}
}
#########################################################
#### No dialog box ###
isCSV <- function(pathFile, errorMSG) {
t = 0
checkIfCsv <- pathFile
checkIfCsv2 <- basename(checkIfCsv)
checkIfCsv3 <- unlist(strsplit(checkIfCsv2, "\\."))
checkIfCsv4 <- checkIfCsv3[length(checkIfCsv3)]
if (checkIfCsv4 %in% c("CSV", "csv")) {
t = 1
return(t)
} else {
#dlgMessage(errorMSG)
return(t)
}
}
#########################################################
## Begin collecting arguments
if (missing(inputData)) {
inputData <- isCSVdlg("Select the CSV file containing the input data", "The input file MUST be in the format of comma-separated value (csv). Please, choose an input file showing the extension .csv.")
inputData <- read.csv(inputData, colClasses = "character", check.names = FALSE)
message("Input file loaded...")
} else {
if (is.data.frame(inputData)) {
message("Data frame loaded...")
} else {
if (is.character(inputData)) {
checkIfCsv <- isCSV(inputData)
if (checkIfCsv == 1) {
inputTest <- file.access(inputData, 0)
if (inputTest == 0) {
inputData = read.csv(inputData, colClasses = "character", check.names = FALSE)
} else {
inputData <- isCSVdlg("Select the CSV file containing the input data", "The input file MUST be in the format of comma-separated value (csv). Please, choose an input file showing the extension .csv.")
inputData <- read.csv(inputData, colClasses = "character", check.names = FALSE)
message("Input file loaded...")
}
} else {
inputData <- isCSVdlg("Select the CSV file containing the input data", "The input file MUST be in the format of comma-separated value (csv). Please, choose an input file showing the extension .csv.")
inputData <- read.csv(inputData, colClasses = "character", check.names = FALSE)
message("Input file loaded...")
}
} else {
inputData <- isCSVdlg("Select the CSV file containing the input data", "The input file MUST be in the format of comma-separated value (csv). Please, choose an input file showing the extension .csv.")
inputData <- read.csv(inputData, colClasses = "character", check.names = FALSE)
message("Input file loaded...")
}
}
}
if (save) {
if (missing(folder)) {
folder = dlgDir(title = "Select the folder where the results will be saved.")$res
} else {
if (is.character(folder)) {
isFolder <- file.access(as.character(folder), 0)
if (isFolder == 0) {
isFolder <- file.info(folder)
if (!isFolder$isdir) {
folder = dlgDir(title = "Select the folder where the results will be saved.")$res
}
} else {
folder = dlgDir(title = "Select the folder where the results will be saved.")$res
}
} else {
folder = dlgDir(title = "Select the folder where the results will be saved.")$res
}
}
}
if (missing(biomass)){
biomass <- c()
} else {
if (is.data.frame(biomass)) {
biomass <- biomass
message("Biomass loaded...")
} else {
if (is.character(biomass)) {
checkIfCsv <- isCSV(biomass)
if (checkIfCsv == 1) {
inputTest <- file.access(biomass, 0)
if (inputTest == 0) {
biomass <- read.csv(biomass, colClasses = "character", check.names = FALSE)
} else {
dlgMessage("Biomass file not accessible.")
biomass <- isCSVdlg("Select the CSV file containing the biomass", "Please, choose a Biomass with the extension .csv.")
biomass <- read.csv(biomass, colClasses = "character", check.names = FALSE)
message("Input biomass file loaded...")
}
} else {
dlgMessage("Biomass file not accessible.")
biomass <- isCSVdlg("Select the CSV file containing the biomass", "Please, choose a Biomass with the extension .csv.")
biomass <- read.csv(inputData, colClasses = "character", check.names = FALSE)
message("Input file loaded...")
}
} else {
dlgMessage("Biomass file not accessible.")
biomass <- isCSVdlg("Select the CSV file containing the biomass", "Please, choose a Biomass with the extension .csv.")
biomass <- read.csv(biomass, colClasses = "character", check.names = FALSE)
message("Input file loaded...")
}
}
}
if (toupper(as.character(inputData[1, 1])) == "REPLICATES") {
replicates <- as.character(inputData[1, ])
inputData <- inputData[-1, ]
rep <- 1
}
if (length(biomass) == 0){
for (i in 2:ncol(inputData)) {
sample.name <- names(inputData)[i]
biomass <- dlgInput(paste("Biomass for sample ", sample.name, ":", sep = ""))$res
if(!length(biomass)){
stop("The process was canceled by the user.")
} else {
biomass <- unlist(strsplit(biomass, "returned:", fixed = TRUE))
biomass <- biomass[length(biomass)]
}
inputData[i] <- as.numeric(inputData[, i])/as.numeric(biomass)
}
} else {
for (i in 2:ncol(inputData)) {
sample.name <- names(inputData[i])
biomass.sample <- biomass[biomass[1] == sample.name]
if (length(biomass.sample) >= 1) {
inputData[i] <- as.numeric(inputData[, i])/as.numeric(biomass.sample[2])
} else {
warning(paste("Biomass was not found for", sample.name))
}
}
}
if (rep == 1) {
inputData <- rbind(replicates, inputData)
}
if (save) {
sheet <- output
store <- file.path(folder, paste(sheet, ".csv", sep = ""))
inputTest <- file.access(store, 0)
if (inputTest == 0) {
addFile <- 1
while(inputTest == 0){
store <- file.path(folder, paste(sheet, addFile, ".csv", sep = ""))
inputTest <- file.access(store, 0)
addFile <- addFile + 1
}
}
write.csv(inputData, file = store, row.names = FALSE)
message("File saved: ", store, "\n")
}
return(inputData)
}
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