MetDNA: MetDNA

#' @title checkData
#' @description Check data.
#' @author Xiaotao Shen
#' \email{shenxt@@sioc.ac.cn}
#' @param data The name of ms1 data.
#' @param sample.info The name of sample information.
#' @param ms2.type The type of MS2 data.
#' @param path The work directory.
#' @return Check result.
#' @export
#'

# checkData(data = "data.csv",
#            sample.info = "sample.info.csv",
#            ms2.type = "msp",
#            path = ".")

setGeneric(name = "checkData",
           def = function(data = "data.csv",
                          sample.info = "sample.info.csv",
                          ms2.type = c("mgf", "mzXML", "msp"),
                          path = "."){


             data.name <- data
             sample.info.name <- sample.info
             data.record <- NULL
             sample.info.record <- NULL
             ms2.file.record <- NULL

             ms2.type <- match.arg(ms2.type)
             cat("Read data.\n")
             cat("--------------------------------------------------------------\n")

             temp.error <- errorDisplay(
               data <- readr::read_csv(file.path(path, data), col_types = readr::cols(),
                                       progress = TRUE),
               error.info = paste("Error: There is no", data, "in", path, ". Please check it.\n"))
             if(class(temp.error) == "try-error") stop("Error")
             data <- as.data.frame(data)

             temp.error <- errorDisplay(
               sample.info <- readr::read_csv(file.path(path, sample.info), col_types = readr::cols(),
                                              progress = TRUE),
               error.info = paste("Error: There is no", sample.info, "in", path, ". Please check it.\n"))
             if(class(temp.error) == "try-error") stop("Error")

             sample.info <- as.data.frame(sample.info)

             ###check the sample.info have - or not, if it has -, change it to .s

             if(length(grep(pattern = "-", sample.info$sample.name)) > 0){
               colnames(data) <- gsub(pattern = "-", replacement = ".", x = colnames(data))
               sample.info$sample.name <- gsub(pattern = "-", replacement = ".", x = sample.info$sample.name)
               readr::write_csv(x = data, path = file.path(path, data.name))
               readr::write_csv(x = sample.info, path = file.path(path, sample.info.name))
             }



             ##check data, NA or space
             if(sum(is.na(data)) > 0){
               cat("Error: There are", sum(is.na(data)), "NAs in you data.\n")
               data.record <- c(data.record, "Error")
             }else{
               # cat("OK: There are no NAs in you data.\n")
               data.record <- c(data.record, "OK")
             }

             if(ifelse(is.na(sum(data == "") > 0), FALSE, sum(data == "") > 0)){
               cat("Error: There are", sum(data == ""), "spaces in you data.\n")
               data.record <- c(data.record, "Error")
             }else{
               # cat("OK: There are no spaces in you data.\n")
               data.record <- c(data.record, "OK")
             }

             ######
             data1 <- data
             data1[is.na(data1)] <- 0
             data1[data1 == ""] <- 0

             temp.error <- errorDisplay(
               data1 <- data1[,setdiff(colnames(data1), c("mz", "rt", "name"))],
               error.info = "Error: The data don't contains 'mz', 'rt' and 'name', please check it.")
             if(class(temp.error) == "try-error") stop("Error")

             temp.error <- errorDisplay(
               zero.per <- apply(data1, 1, function(x){
                 sum(x == 0)/ncol(data1)
               }),
               error.info = "Error: The data contains other non-numeric columns, please check it.")
             if(class(temp.error) == "try-error") stop("Error")

             if(sum(zero.per > 0.5) > 0){
               cat("Warning: There are peaks with zero ratio > 50% in you data.\n")
               data.record <- c(data.record, "Warning")
             }

             #####

             ##check data, component
             data.col.name <- colnames(data)
             if(length(data.col.name) < 7){
               cat("Warning: There are less than 4 samples in your data, please check it.\n")
               data.record <- c(data.record, "Warning")
             }else{
               cat("There are", length(data.col.name) - 3, "samples in your data.\n")
               data.record <- c(data.record, "OK")
             }

             if(data.col.name[1] != "name"){
               cat("Error: The first column of data is not 'name'.\n")
               data.record <- c(data.record, "Error")
             }else{
               # cat("OK: The first column of data is name.\n")
               data.record <- c(data.record, "OK")
             }

             if(data.col.name[2] != "mz"){
               cat("Error: The second column of data is not 'mz'.\n")
               data.record <- c(data.record, "Error")
             }else{
               # cat("OK: The second column of data is mz.\n")
               data.record <- c(data.record, "OK")
             }

             if(data.col.name[3] != "rt"){
               cat("Error: The third column of data is not 'rt'.\n")
               data.record <- c(data.record, "Error")
             }else{
               # cat("OK: The third column of data is not rt.\n")
               data.record <- c(data.record, "OK")
             }


             ##check data, RT
             if(any(data.col.name == "rt")){
               rt <- as.numeric(data$rt)
               if(max(rt) < 60){
                 cat("Warning: Please confirm that the rt is measured in seconds,\n")
                 data.record <- c(data.record, "Warning")
               }
               cat("RT range is", range(rt), ".\n")
             }

             cat("--------------------------------------------------------------\n")
             ##check sample.info
             if(ncol(sample.info) > 2){
               cat("Error: The smple.info has more than two columns. Please check it.\n")
               sample.info.record <- c(sample.info.record, "Error")
             }

             if(colnames(sample.info)[1] != "sample.name"){
               cat("Error: The first column name of sample.info must be 'sample.name'. Please check it.\n")
               sample.info.record <- c(sample.info.record, "Error")
             }else{
               sample.info.record <- c(sample.info.record, "OK")
             }

             if(colnames(sample.info)[2] != "group"){
               cat("Error: The second column name of sample.info must be 'group'. Please check it.\n")
               sample.info.record <- c(sample.info.record, "Error")
             }else{
               sample.info.record <- c(sample.info.record, "OK")
             }

             if(sum(is.na(sample.info)) > 0){
               cat("Error: There are", sum(is.na(sample.info)), "NAs in you sample.info.\n")
               sample.info.record <- c(sample.info.record, "Error")
             }else{
               # cat("OK: There are no NAs in you sample.info.\n")
               sample.info.record <- c(sample.info.record, "OK")
             }

             if(ifelse(is.na(sum(sample.info == "") > 0), FALSE, sum(sample.info == "") > 0)){
               cat("Error: There are", sum(sample.info == ""), "spaces in you sample.info.\n")
               sample.info.record <- c(sample.info.record, "Error")
             }else{
               # cat("OK: There are no spaces in you sample.info.\n")
               sample.info.record <- c(sample.info.record, "OK")
             }


             group <-  table(as.character(sample.info[,2]))
             group1 <- matrix(group, nrow = 1)
             colnames(group1) <- names(group)
             rownames(group1) <- "Number"

             cat("Group information:\n")
             print(group1)


             if(any(group1[1,] < 2)){
               cat("Warning: ","Group", group1[1,which(group1[,1] < 3)],
                   ifelse(length(which(group1[,1] < 3)) > 1, "have", "has"),
                   "less than 3 samples, please check it.\n"
               )
               sample.info.record <- c(sample.info.record, "Warning")
             }else{
               sample.info.record <- c(sample.info.record, "OK")
             }


             data.col.name <- setdiff(data.col.name, c("name", "mz", "rt"))
             sample.name <- as.character(sample.info[,1])

             if(any(sort(data.col.name) != sort(sample.name))){
               cat("Error: The sample names in data and sample.info are not same.\n")
               sample.info.record <- c(sample.info.record, "Error")
             }else{
               sample.info.record <- c(sample.info.record, "OK")
             }


             ###if the name of sample is begin with number, add "Sample" before it
             data.col.name <- setdiff(data.col.name, c("name", "mz", "rt"))
             sample.name <- as.character(sample.info[,1])

             if(any(substr(x = sample.name, start = 1, stop = 1) %in% 0:9)){
               cat("Warning: The names of samples should not start with a number.\n")
               sample.info.record <- c(sample.info.record, "Warning")

               idx1 <- which(substr(x = sample.name, start = 1, stop = 1) %in% 0:9)
               idx2 <- which(substr(x = data.col.name, start = 1, stop = 1) %in% 0:9)

               sample.name[idx1] <- paste("Sample", sample.name[idx1], sep = "")
               data.col.name[idx2] <- paste("Sample", data.col.name[idx2], sep = "")

               sample.info[,1] <- sample.name
               colnames(data)[-which(colnames(data) %in% c("name", "mz", "rt"))] <- data.col.name
               readr::write_csv(data, file.path(path, "data.csv"))
               readr::write_csv(sample.info, file.path(path, "sample.info.csv"))

             }else{
               sample.info.record <- c(sample.info.record, "OK")
             }

             cat("--------------------------------------------------------------\n")
             ##ms2.file
             switch(ms2.type,
                    "mgf" = {ms2.file <- grep("mgf", dir(path), value = TRUE)},
                    "msp" = {ms2.file <- grep("msp", dir(path), value = TRUE)},
                    "mzXML" = {ms2.file <- grep("mzXML", dir(path), value = TRUE)})

             if(length(ms2.file) == 0){
               cat("Error: There are no ms2 data.\n")
               ms2.file.record <- c(ms2.file.record, "Error")
             }else{
               cat("There are", length(ms2.file), "ms2 data.\n")
               ms2.file.record <- c(ms2.file.record, "OK")
               cat("Total size of ms2 data is", sum(file.size(ms2.file)/(1024*1024)), "M.\n")
             }

             cat("--------------------------------------------------------------\n")
             cat("Summary:\n")

             stat <- lapply(list(data.record, sample.info.record, ms2.file.record),
                            function(x) {
                              return(c(ifelse(all(x!="Error"), "Valid", "Invalid"),
                                       sum(x=="OK"), sum(x=="Warning"), sum(x=="Error")))
                            })
             stat <- do.call(rbind, stat)
             colnames(stat) <- c("Check result","OK", "Warning", "Error")
             rownames(stat) <- c("data", "sample.info", "ms2.file")

             print(stat, quote = FALSE)
             cat("\n")

             cat("\n")
             cat("data:\n")
             if(all(data.record != "Error")){
               cat("data is valid.\n")
             }else{
               if(sum(data.record == "Warning") > 0){
                 cat("There", ifelse(sum(data.record == "Warning") > 1, "are", "is"),
                     sum(data.record == "Warning"),
                     ifelse(sum(data.record == "Warning") > 1, "Warnings", "Warning"),
                     "in your data. Please check it according to the information.\n")
               }

               if(sum(data.record == "Error") > 0){
                 cat("There", ifelse(sum(data.record == "Error") > 1, "are", "is"),
                     sum(data.record == "Error"),
                     ifelse(sum(data.record == "Error") > 1, "Errors", "Error"),
                     "in your data. Please check it according to the information.\n")
               }

             }



             cat("\n")
             cat("sample.info:\n")
             if(all(sample.info.record != "Error")){
               cat("sample.info is valid.\n")
             }else{
               if(sum(sample.info.record == "Warning") > 0){
                 cat("There", ifelse(sum(sample.info.record == "Warning") > 1, "are", "is"),
                     sum(sample.info.record == "Warning"),
                     ifelse(sum(sample.info.record == "Warning") > 1, "Warnings", "Warning"),
                     "in your sample.info. Please check it according to the information.\n")
               }

               if(sum(sample.info.record == "Error") > 0){
                 cat("There", ifelse(sum(sample.info.record == "Error") > 1, "are", "is"),
                     sum(sample.info.record == "Error"),
                     ifelse(sum(sample.info.record == "Error") > 1, "Errors", "Error"),
                     "in your sample.info. Please check it according to the information.\n")
               }

             }

             cat("\n")
             cat("ms2.file:\n")
             if(all(ms2.file.record != "Error")){
               cat("ms2.file are valid.\n")
             }else{
               if(sum(ms2.file.record == "Warning") > 0){
                 cat("There", ifelse(sum(ms2.file.record == "Warning") > 1, "are", "is"),
                     sum(ms2.file.record == "Warning"),
                     ifelse(sum(ms2.file.record == "Warning") > 1, "Warnings", "Warning"),
                     "in your ms2.file. Please check it according to the information.\n")
               }

               if(sum(ms2.file.record == "Error") > 0){
                 cat("There", ifelse(sum(ms2.file.record == "Error") > 1, "are", "is"),
                     sum(ms2.file.record == "Error"),
                     ifelse(sum(ms2.file.record == "Error") > 1, "Errors", "Error"),
                     "in your ms2.file. Please check it according to the information.\n")
               }

             }
             stat <- stat
           })