R/check_data.R

In jaspershen/metflow2: Comprehensitive tools for metabolomics data processing and data analysis

#' @title check_data
#' @description Check data format.
#' @author Xiaotao Shen
#' \email{shenxt1990@@163.com}
#' @param data MS1 data tables.
#' @param sample.info Name of sample information.
#' @param path Work directory.
#' @return Notice of data checking.
#' @export

check_data = function(data = c("batch1.csv", "batch2.csv"),
                     sample.info = "sample.information.csv",
                     path = "."){
  sample.info.record <- NULL
  cat("Reading data...\n")
  cat("--------------------------------------------------------------\n")
  data <- lapply(data, function(x) {
    as.data.frame(readr::read_csv(
      file.path(path, x),
      col_types = readr::cols(),
      progress = TRUE
    ))
  })
  
  sample.info <-
    readr::read_csv(file.path(path, sample.info),
                    col_types = readr::cols(),
                    progress = TRUE)
  
  sample.info <- as.data.frame(sample.info)
  #####
  
  ##check data, component
  data.record <- lapply(seq_along(data), function(x) {
    temp.data.record <- NULL
    data.col.name <- colnames(data[[x]])
    if (all(data.col.name != "name")) {
      cat(crayon::red(clisymbols::symbol$cross,"Error: No name in data.\n"))
      temp.data.record <- c(temp.data.record, "Error")
    } else{
      # cat("OK: The first column of data is name.\n")
      temp.data.record <- c(temp.data.record, "OK")
    }
    
    if (all(data.col.name != "mz")) {
      cat(crayon::red(clisymbols::symbol$cross,"Error: No mz in data.\n"))
      temp.data.record <- c(temp.data.record, "Error")
    } else{
      # cat("OK: The second column of data is mz.\n")
      temp.data.record <- c(temp.data.record, "OK")
    }
    
    if (all(data.col.name != "rt")) {
      cat(crayon::red(clisymbols::symbol$cross,"Error: No rt in data.\n"))
      temp.data.record <- c(temp.data.record, "Error")
    } else{
      # cat("OK: The third column of data is not rt.\n")
      temp.data.record <- c(temp.data.record, "OK")
    }
    temp.data.record
  })
  
  cat("--------------------------------------------------------------\n")
  ##check sample.info
  if (sum(is.na(sample.info)) > 0) {
    cat(crayon::red(clisymbols::symbol$cross,
                    "Error: There are", sum(is.na(sample.info)), "NAs in your 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(crayon::red(clisymbols::symbol$cross,
                    "Error: There are",
                    sum(sample.info == ""),
                    "spaces in you sample.info.\n"))
    sample.info.record <- c(sample.info.record, "Error")
  } else{
    sample.info.record <- c(sample.info.record, "OK")
  }
  
  if (colnames(sample.info)[1] != "sample.name") {
    cat(crayon::red(clisymbols::symbol$cross,
                    "Error: The column 1 of sample information must be sample.name\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")
  }
  
  if (colnames(sample.info)[2] != "injection.order") {
    cat(crayon::red(clisymbols::symbol$cross,
                    "Error: The column 2 of sample information must be injection.order\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")
  }
  
  if (colnames(sample.info)[3] != "class") {
    cat(crayon::red(clisymbols::symbol$cross,
                    "Error: The column 3 of sample information must be class"))
    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")
  }
  
  if (colnames(sample.info)[4] != "batch") {
    cat(crayon::red(clisymbols::symbol$cross,
                    "Error: The column 4 of sample information must be batch"))
    sample.info.record <- c(sample.info.record, "Error")
  } else{
    # cat("OK: There are no spaces in you sample.info.\n")
    sample.info.record <- c(sample.info.record, "OK")
    if (any(table(sample.info[, "batch"]) <= 5)) {
      cat(crayon::yellow(clisymbols::symbol$warning,
                         "There are some batch only have less than 5 samples. Please check it.\n"))
      sample.info.record <-
        c(sample.info.record, "Error")
    }
  }
  
  if (colnames(sample.info)[5] != "group") {
    cat(crayon::red(clisymbols::symbol$cross,
                    "Error: The column 5 of sample information must be group"))
    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")
  }
  
  class <-  unique(as.character(sample.info[, 3]))
  if (any(c("QC", "Subject") %in% class)) {
    sample.info.record <- c(sample.info.record, "OK")
  } else{
    cat(crayon::red(clisymbols::symbol$cross,
                    "Error: The class of sample.information must be QC and Subject.\n"))
    sample.info.record <- c(sample.info.record, "Error")
  }
  
  sample.idx <- match(sample.info$sample.name,
                      unique(unlist(lapply(data, function(x)
                        colnames(x)))))
  
  if (any(is.na(sample.idx))) {
    cat(crayon::red(clisymbols::symbol$cross,
                    "Error: The sample names in sample.inforamtion and data are not same.\n"))
    sample.info.record <- c(sample.info.record, "Error")
  } else{
    sample.info.record <- c(sample.info.record, "OK")
  }
  
  cat("--------------------------------------------------------------\n")
  cat("Summary:\n")
  
  stat <- lapply(c(data.record, list(sample.info.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)
  stat <- as.data.frame(stat)
  colnames(stat) <-
    c("Check result", "OK", "Warning", "Error")
  rownames(stat)[nrow(stat)] <- "sample.info"
  rownames(stat)[1:(nrow(stat) - 1)] <-
    paste("batch", 1:(nrow(stat) - 1), sep = "")
  
  print(stat, quote = FALSE)
  cat("\n")
  cat("\n")
  cat("data:\n")
  for (idx in 1:length(data.record)) {
    if (all(data.record[idx] != "Error")) {
      cat(paste("Batch", idx), "is valid.\n")
    } else{
      if (sum(data.record[idx] == "Warning") > 0) {
        cat(
          "There",
          ifelse(sum(data.record[idx] == "Warning") > 1, "are", "is"),
          sum(data.record[idx] == "Warning"),
          ifelse(sum(data.record[idx] == "Warning") > 1, "Warnings", "Warning"),
          "in your",
          paste("Batch", idx),
          ".Please check it according to the information.\n"
        )
      }
      
      if (sum(data.record[idx] == "Error") > 0) {
        cat(
          "There",
          ifelse(sum(data.record[idx] == "Error") > 1, "are", "is"),
          sum(data.record[idx] == "Error"),
          ifelse(sum(data.record[idx] == "Error") > 1, "Errors", "Error"),
          "in your",
          paste("Batch", idx),
          ".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"
      )
    }
  }
  stat <- as.data.frame(stat)
  stat[, 1] <- as.character(stat[, 1])
  stat[, 2] <- as.numeric(stat[, 2])
  stat[, 3] <- as.numeric(stat[, 3])
  invisible(stat)
}




#' @title checkData
#' @description Check data format.
#' @author Xiaotao Shen
#' \email{shenxt1990@@163.com}
#' @param data MS1 data tables.
#' @param sample.info Name of sample information.
#' @param path Work directory.
#' @return Notice of data checking.
#' @export

checkData = function(data = c("batch1.csv", "batch2.csv"),
                     sample.info = "sample.information.csv",
                     path = "."){
  cat(crayon::yellow("checkData() is deprecated, please use the check_data().\n"))
  sample.info.record <- NULL
  cat("Reading data...\n")
  cat("--------------------------------------------------------------\n")
  data <- lapply(data, function(x) {
    as.data.frame(readr::read_csv(
      file.path(path, x),
      col_types = readr::cols(),
      progress = TRUE
    ))
  })
  
  sample.info <-
    readr::read_csv(file.path(path, sample.info),
                    col_types = readr::cols(),
                    progress = TRUE)
  
  sample.info <- as.data.frame(sample.info)
  #####
  
  ##check data, component
  data.record <- lapply(seq_along(data), function(x) {
    temp.data.record <- NULL
    data.col.name <- colnames(data[[x]])
    if (all(data.col.name != "name")) {
      cat(crayon::red(clisymbols::symbol$cross,"Error: No name in data.\n"))
      temp.data.record <- c(temp.data.record, "Error")
    } else{
      # cat("OK: The first column of data is name.\n")
      temp.data.record <- c(temp.data.record, "OK")
    }
    
    if (all(data.col.name != "mz")) {
      cat(crayon::red(clisymbols::symbol$cross,"Error: No mz in data.\n"))
      temp.data.record <- c(temp.data.record, "Error")
    } else{
      # cat("OK: The second column of data is mz.\n")
      temp.data.record <- c(temp.data.record, "OK")
    }
    
    if (all(data.col.name != "rt")) {
      cat(crayon::red(clisymbols::symbol$cross,"Error: No rt in data.\n"))
      temp.data.record <- c(temp.data.record, "Error")
    } else{
      # cat("OK: The third column of data is not rt.\n")
      temp.data.record <- c(temp.data.record, "OK")
    }
    temp.data.record
  })
  
  cat("--------------------------------------------------------------\n")
  ##check sample.info
  if (sum(is.na(sample.info)) > 0) {
    cat(crayon::red(clisymbols::symbol$cross,
                    "Error: There are", sum(is.na(sample.info)), "NAs in your 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(crayon::red(clisymbols::symbol$cross,
                    "Error: There are",
                    sum(sample.info == ""),
                    "spaces in you sample.info.\n"))
    sample.info.record <- c(sample.info.record, "Error")
  } else{
    sample.info.record <- c(sample.info.record, "OK")
  }
  
  if (colnames(sample.info)[1] != "sample.name") {
    cat(crayon::red(clisymbols::symbol$cross,
                    "Error: The column 1 of sample information must be sample.name\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")
  }
  
  if (colnames(sample.info)[2] != "injection.order") {
    cat(crayon::red(clisymbols::symbol$cross,
                    "Error: The column 2 of sample information must be injection.order\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")
  }
  
  if (colnames(sample.info)[3] != "class") {
    cat(crayon::red(clisymbols::symbol$cross,
                    "Error: The column 3 of sample information must be class"))
    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")
  }
  
  if (colnames(sample.info)[4] != "batch") {
    cat(crayon::red(clisymbols::symbol$cross,
                    "Error: The column 4 of sample information must be batch"))
    sample.info.record <- c(sample.info.record, "Error")
  } else{
    # cat("OK: There are no spaces in you sample.info.\n")
    sample.info.record <- c(sample.info.record, "OK")
    if (any(table(sample.info[, "batch"]) <= 5)) {
      cat(crayon::yellow(clisymbols::symbol$warning,
                         "There are some batch only have less than 5 samples. Please check it.\n"))
      sample.info.record <-
        c(sample.info.record, "Error")
    }
  }
  
  if (colnames(sample.info)[5] != "group") {
    cat(crayon::red(clisymbols::symbol$cross,
                    "Error: The column 5 of sample information must be group"))
    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")
  }
  
  class <-  unique(as.character(sample.info[, 3]))
  if (any(c("QC", "Subject") %in% class)) {
    sample.info.record <- c(sample.info.record, "OK")
  } else{
    cat(crayon::red(clisymbols::symbol$cross,
                    "Error: The class of sample.information must be QC and Subject.\n"))
    sample.info.record <- c(sample.info.record, "Error")
  }
  
  sample.idx <- match(sample.info$sample.name,
                      unique(unlist(lapply(data, function(x)
                        colnames(x)))))
  
  if (any(is.na(sample.idx))) {
    cat(crayon::red(clisymbols::symbol$cross,
                    "Error: The sample names in sample.inforamtion and data are not same.\n"))
    sample.info.record <- c(sample.info.record, "Error")
  } else{
    sample.info.record <- c(sample.info.record, "OK")
  }
  
  cat("--------------------------------------------------------------\n")
  cat("Summary:\n")
  
  stat <- lapply(c(data.record, list(sample.info.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)
  stat <- as.data.frame(stat)
  colnames(stat) <-
    c("Check result", "OK", "Warning", "Error")
  rownames(stat)[nrow(stat)] <- "sample.info"
  rownames(stat)[1:(nrow(stat) - 1)] <-
    paste("batch", 1:(nrow(stat) - 1), sep = "")
  
  print(stat, quote = FALSE)
  cat("\n")
  cat("\n")
  cat("data:\n")
  for (idx in 1:length(data.record)) {
    if (all(data.record[idx] != "Error")) {
      cat(paste("Batch", idx), "is valid.\n")
    } else{
      if (sum(data.record[idx] == "Warning") > 0) {
        cat(
          "There",
          ifelse(sum(data.record[idx] == "Warning") > 1, "are", "is"),
          sum(data.record[idx] == "Warning"),
          ifelse(sum(data.record[idx] == "Warning") > 1, "Warnings", "Warning"),
          "in your",
          paste("Batch", idx),
          ".Please check it according to the information.\n"
        )
      }
      
      if (sum(data.record[idx] == "Error") > 0) {
        cat(
          "There",
          ifelse(sum(data.record[idx] == "Error") > 1, "are", "is"),
          sum(data.record[idx] == "Error"),
          ifelse(sum(data.record[idx] == "Error") > 1, "Errors", "Error"),
          "in your",
          paste("Batch", idx),
          ".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"
      )
    }
  }
  stat <- as.data.frame(stat)
  stat[, 1] <- as.character(stat[, 1])
  stat[, 2] <- as.numeric(stat[, 2])
  stat[, 3] <- as.numeric(stat[, 3])
  invisible(stat)
}