diff --git a/R/eem_utils.R b/R/eem_utils.R
index 5f1dd9f..5984b51 100644
--- a/R/eem_utils.R
+++ b/R/eem_utils.R
@@ -1,635 +1,635 @@
-#' @importFrom graphics par plot text filled.contour title
-#' @importFrom viridis viridis
-.plot_eem <- function(x, show_peaks, ...) {
-  filled.contour(
-    y = x$em,
-    x = x$ex,
-    z = t(x$x),
-    plot.title = title(
-      main = paste(x$sample, "\n", attr(x, "manucafturer"), sep = ""),
-      xlab = "Excitation (nm.)",
-      ylab = "Emission (nm.)"
-    ),
-    key.title = title("Fluorescence\nintensity"),
-    color.palette = viridis::viridis,
-    nlevels = 7,
-    ...
-  )
-  #
-  # fields::image.plot(y = x$em,
-  #              x = x$ex,
-  #              z = t(x$x),
-  #              main = paste(x$sample, "\n", attr(x, "manucafturer"), sep = ""),
-  #              xlab = "Excitation (nm.)",
-  #              ylab = "Emission (nm.)",
-  #              legend.lab = "Fluorescence intensity",
-  #              col = viridis::viridis(256),
-  #              nlevel = 7,
-  #
-  #              ...)
-
-  if (show_peaks) {
-    coble_ex_peak <- list(b = 275, t = 275, a = 260, m = 312, c = 350)
-    coble_em_peak <- list(b = 310, t = 340, a = 420, m = 400, c = 450)
-
-    text(coble_ex_peak$b, coble_em_peak$b, "B", font = 2, cex = 1)
-    text(coble_ex_peak$t, coble_em_peak$t, "T", font = 2, cex = 1)
-    text(coble_ex_peak$a, coble_em_peak$a, "A", font = 2, cex = 1)
-    text(coble_ex_peak$m, coble_em_peak$m, "M", font = 2, cex = 1)
-    text(coble_ex_peak$c, coble_em_peak$c, "C", font = 2, cex = 1)
-  }
-}
-
-#' Surface plot of eem
-#'
-#' @param x An object of class \code{eemlist}.
-#' @param which An integer representing the index of eem to be plotted.
-#' @param ... Extra arguments for \code{image.plot}.
-#' @param show_peaks Boolean indicating if Cobble's peaks should be displayed on
-#'   the surface plot. Default is FALSE.
-#' @param interactive If \code{TRUE} a Shiny app will start to visualize EEMS.
-#'
-#' @export
-#' @examples
-#' folder <- system.file("extdata/cary/scans_day_1/", package = "eemR")
-#' eem <- eem_read(folder, import_function = "cary")
-#'
-#' plot(eem, which = 3)
-plot.eemlist <- function(x, which = 1,
-                         interactive = FALSE, show_peaks = FALSE, ...) {
-  stopifnot(which <= length(x))
-
-  if (interactive) {
-    .plot_shiny(x)
-  } else {
-    .plot_eem(x[[which]], show_peaks, ...)
-  }
-}
-
-eem_as_summary <- function(object) {
-  df <- data.frame(
-    sample = object$sample,
-    ex_min = min(object$ex),
-    ex_max = max(object$ex),
-    em_min = min(object$em),
-    em_max = max(object$em),
-    is_blank_corrected = attr(object, "is_blank_corrected"),
-    is_scatter_corrected = attr(object, "is_scatter_corrected"),
-    is_ife_corrected = attr(object, "is_ife_corrected"),
-    is_raman_normalized = attr(object, "is_raman_normalized")
-  )
-
-  return(df)
-}
-
-#' Display summary of an eemlist object
-#'
-#' @param x An object of class \code{eemlist}.
-#' @param ... Extra arguments.
-#' @template template_summary
-#'
-#' @export
-#' @examples
-#' folder <- system.file("extdata/cary", package = "eemR")
-#' eem <- eem_read(folder, recursive = TRUE, import_function = "cary")
-#'
-#' print(eem)
-print.eemlist <- function(x, ...) {
-  stopifnot(class(x) == "eemlist")
-
-  df <- lapply(x, eem_as_summary)
-  df <- do.call(rbind, df)
-
-  print(df)
-
-  invisible(df)
-}
-
-#' Display summary of an eemlist object
-#'
-#' @param object An object of class \code{eemlist}.
-#' @param ... Extra arguments.
-#' @template template_summary
-#' @export
-#' @examples
-#' folder <- system.file("extdata/cary", package = "eemR")
-#' eem <- eem_read(folder, recursive = TRUE, import_function = "cary")
-#'
-#' summary(eem)
-summary.eemlist <- function(object, ...) {
-  stopifnot(class(object) == "eemlist")
-
-  df <- lapply(object, eem_as_summary)
-  df <- do.call(rbind, df)
-
-  print(df)
-
-  invisible(df)
-}
-
-
-#' Cut emission and/or excitation wavelengths from EEMs
-#'
-#' @template template_eem
-#' @param ex A numeric vector of excitation wavelengths to be removed.
-#' @param em A numeric vector of emission wavelengths to be removed.
-#' @param exact Logical. If TRUE, only wavelengths matching \code{em} and/or
-#'   \code{ex} will be removed. If FALSE, all wavelengths in the range of
-#'   \code{em} and/or \code{ex} will be removed.
-#' @param fill_with_na Logical. If TRUE, fluorescence values at specified
-#'   wavelengths will be replaced with NA. If FALSE, these values will be
-#'   removed.
-#' @export
-#' @examples
-#' # Open the fluorescence eem
-#' file <- system.file("extdata/cary/scans_day_1/", "sample1.csv", package = "eemR")
-#'
-#' eem <- eem_read(file, import_function = "cary")
-#' plot(eem)
-#'
-#' # Cut few excitation wavelengths
-#' eem <- eem_cut(eem, ex = c(220, 225, 230, 230))
-#' plot(eem)
-#'
-#' eem <- eem_read(file, import_function = "cary")
-#' eem <- eem_cut(eem, em = 350:400, fill_with_na = TRUE)
-#' plot(eem)
-eem_cut <- function(eem, ex, em, exact = TRUE, fill_with_na = FALSE) {
-  stopifnot(
-    .is_eemlist(eem) | .is_eem(eem)
-  )
-
-  ## It is a list of eems, then call lapply
-  if (.is_eemlist(eem)) {
-    res <-
-      lapply(
-        eem,
-        eem_cut,
-        ex = ex,
-        em = em,
-        exact = exact,
-        fill_with_na = fill_with_na
-      )
-
-    class(res) <- class(eem)
-
-    return(res)
-  }
-
-  ## Maybe round em and ex wavelengths
-
-  if (!missing(ex)) {
-    stopifnot(
-      is.numeric(ex),
-      all(ex >= 0)
-    )
-
-    if (exact) {
-      index <- which(eem$ex %in% ex)
-    } else {
-      index <- which(is_between(
-        eem$ex,
-        min(ex, na.rm = TRUE),
-        max(ex, na.rm = TRUE)
-      ))
-    }
-
-    if (length(index != 0)) {
-      if (fill_with_na) {
-        # eem$ex[index] <- NA
-        eem$x[, index] <- NA
-      }
-      else {
-        eem$ex <- eem$ex[-index]
-        eem$x <- eem$x[, -index]
-      }
-    }
-  }
-
-  if (!missing(em)) {
-    stopifnot(
-      is.numeric(em),
-      all(em >= 0)
-    )
-
-    if (exact) {
-      index <- which(eem$em %in% em)
-    } else {
-      index <- which(is_between(
-        eem$em,
-        min(em, na.rm = TRUE),
-        max(em, na.rm = TRUE)
-      ))
-    }
-
-    if (length(index != 0)) {
-      if (fill_with_na) {
-        # eem$em[index] <- NA
-        eem$x[index, ] <- NA
-      }
-      else {
-        eem$em <- eem$em[-index]
-        eem$x <- eem$x[-index, ]
-      }
-    }
-  }
-
-  return(eem)
-}
-
-#' Set Excitation and/or Emission wavelengths
-#'
-#' This function allows to manually specify either excitation or emission vector
-#' of wavelengths in EEMs. This function is mostly used with spectrophotometers
-#' such as Shimadzu that do not include excitation wavelengths in fluorescence
-#' files.
-#'
-#' @template template_eem
-#' @param ex A numeric vector of excitation wavelengths.
-#' @param em A numeric vector of emission wavelengths.
-#'
-#' @examples
-#' folder <- system.file("extdata/shimadzu", package = "eemR")
-#'
-#' eem <- eem_read(folder, import_function = "shimadzu")
-#' eem <- eem_set_wavelengths(eem, ex = seq(230, 450, by = 5))
-#'
-#' plot(eem)
-#' @export
-
-eem_set_wavelengths <- function(eem, ex, em) {
-  stopifnot(.is_eemlist(eem) | .is_eem(eem))
-
-  ## It is a list of eems, then call lapply
-  if (.is_eemlist(eem)) {
-    res <- lapply(eem, eem_set_wavelengths, ex = ex, em = em)
-
-    class(res) <- class(eem)
-
-    return(res)
-  }
-
-  if (!missing(ex)) {
-    stopifnot(
-      is.vector(ex),
-      is.numeric(ex),
-      identical(length(ex), ncol(eem$x)),
-      all(ex == cummax(ex))
-    ) ## Monotonously increasing
-
-    eem$ex <- ex
-  }
-
-  if (!missing(em)) {
-    stopifnot(
-      is.vector(em),
-      is.numeric(em),
-      identical(length(em), nrow(eem$x)),
-      all(em == cummax(em))
-    ) ## Monotonously increasing
-
-    eem$em <- em
-  }
-
-  return(eem)
-}
-
-#' Extract EEM samples
-#'
-#' @template template_eem
-#'
-#' @param sample Either numeric of character vector. See \code{details} for more
-#'   information.
-#'
-#' @param keep logical. If TRUE, the specified \code{sample} will be returned.
-#'   If FALSE, they will be removed.
-#'
-#' @param ignore_case Logical, should sample name case should be ignored (TRUE)
-#'   or not (FALSE). Default is FALSE.
-#'
-#' @param verbose Logical determining if removed/extracted eems should be
-#'   printed on screen.
-#'
-#' @details \code{sample} argument can be either numeric or character vector. If
-#'   it is numeric, samples at specified index will be removed.
-#'
-#'   If \code{sample} is character, regular expression will be used and all
-#'   sample names that have a partial or complete match with the expression will
-#'   be removed. See \code{examples} for more details.
-#'
-#' @examples
-#' folder <- system.file("extdata/cary/scans_day_1", package = "eemR")
-#' eems <- eem_read(folder, import_function = "cary")
-#'
-#' eems
-#'
-#' # Remove first and third samples
-#' eem_extract(eems, c(1, 3))
-#'
-#' # Remove everything except first and third samples
-#' eem_extract(eems, c(1, 3), keep = TRUE)
-#'
-#' # Remove all samples containing "3" in their names.
-#' eem_extract(eems, "3")
-#'
-#' # Remove all samples containing either character "s" or character "2" in their names.
-#' eem_extract(eems, c("s", "2"))
-#'
-#' # Remove all samples containing "blank" or "nano"
-#' eem_extract(eems, c("blank", "nano"))
-#' @export
-eem_extract <- function(eem, sample, keep = FALSE, ignore_case = FALSE,
-                        verbose = TRUE) {
-  stopifnot(
-    class(eem) == "eemlist",
-    is.character(sample) | is.numeric(sample)
-  )
-
-  sample_names <- unlist(lapply(eem, function(x) {
-    x$sample
-  }))
-
-  ## Sample number
-  if (is.numeric(sample)) {
-    stopifnot(all(is_between(sample, 1, length(eem))))
-
-    to_remove <- ifelse(rep(keep, length(sample)),
-      setdiff(1:length(eem), sample),
-      sample
-    )
-
-    eem[to_remove] <- NULL
-
-    if (verbose) {
-      cat(
-        ifelse(keep, "Extracted sample(s):", "Removed sample(s):"),
-        sample_names[sample], "\n"
-      )
-    }
-  }
-
-  ## Regular expression
-  if (is.character(sample)) {
-    to_remove <- grepl(paste(sample, collapse = "|"),
-      sample_names,
-      ignore.case = ignore_case
-    )
-
-    eem[xor(to_remove, keep)] <- NULL
-
-    if (verbose) {
-      if (all(to_remove == FALSE)) {
-        cat("Nothing to remove.")
-      }
-      else {
-        cat(
-          ifelse(keep, "Extracted sample(s):", "Removed sample(s):"),
-          sample_names[to_remove], "\n"
-        )
-      }
-    }
-  }
-
-  return(eem)
-}
-
-#' The names of an eem or eemlist objects
-#'
-#' @template template_eem
-#'
-#' @return A character vector containing the names of the EEMs.
-#'
-#' @examples
-#' file <- system.file("extdata/cary/", package = "eemR")
-#' eem <- eem_read(file, recursive = TRUE, import_function = "cary")
-#'
-#' eem_names(eem)
-#' @export
-eem_names <- function(eem) {
-  stopifnot(.is_eemlist(eem) | .is_eem(eem))
-
-  ## It is a list of eems, then call lapply
-  if (.is_eemlist(eem)) {
-    res <- unlist(lapply(eem, eem_names))
-
-    return(res)
-  }
-
-  return(eem$sample)
-}
-
-
-#' Set the sample names of an eem or eemlist objects
-#'
-#' @param x An object of class \code{eem} or \code{eemlist}.
-#' @param value A character vector with new sample names. Must be equal
-#'   in length to the number of samples in the \code{eem} or \code{eemlist}.
-#'
-#' @return An \code{eem} or \code{eemlist}.
-#'
-#' @examples
-#' folder <- system.file("extdata/cary/scans_day_1", package = "eemR")
-#' eems <- eem_read(folder, import_function = "cary")
-#'
-#' eem_names(eems)
-#' eem_names(eems) <- c("a", "b", "c", "d")
-#' eem_names(eems)
-#' @export
-`eem_names<-` <- function(x, value) {
-  stopifnot(.is_eemlist(x) | .is_eem(x))
-
-  if (.is_eemlist(x)) {
-    stopifnot(length(x) == length(value))
-
-    res <- Map(`eem_names<-`, x[], value)
-
-    class(res) <- "eemlist"
-    return(res)
-  }
-
-  stopifnot(length(value) == 1)
-
-  x$sample <- value
-
-  class(x) <- "eem"
-  return(x)
-}
-
-#' Bind eem or eemlist
-#'
-#' Function to bind EEMs that have been loaded from different folders or have
-#' been processed differently.
-#'
-#' @param ... One or more object of class \code{eemlist}.
-#'
-#' @return An object of \code{eemlist}.
-#' @export
-#'
-#' @examples
-#' file <- system.file("extdata/cary/scans_day_1/", "sample1.csv", package = "eemR")
-#' eem <- eem_read(file, import_function = "cary")
-#'
-#' eem <- eem_bind(eem, eem)
-eem_bind <- function(...) {
-  eem <- list(...)
-
-  list_classes <- unlist(lapply(eem, function(x) {
-    class(x)
-  }))
-
-  stopifnot(all(list_classes %in% c("eem", "eemlist")))
-
-  eem <- lapply(eem, my_unlist)
-  eem <- unlist(eem, recursive = FALSE)
-
-  class(eem) <- "eemlist"
-
-  return(eem)
-}
-
-my_unlist <- function(x) {
-  if (class(x) == "eem") {
-    x <- list(x)
-
-    class(x) <- "eemlist"
-
-    return(x)
-  } else {
-    return(x)
-  }
-}
-
-.is_eemlist <- function(eem) {
-  ifelse(class(eem) == "eemlist", TRUE, FALSE)
-}
-
-.is_eem <- function(eem) {
-  ifelse(class(eem) == "eem", TRUE, FALSE)
-}
-
-.plot_shiny <- function(eem) {
-  metrics <- dplyr::left_join(eem_coble_peaks(eem, verbose = FALSE),
-    eem_biological_index(eem, verbose = FALSE),
-    by = "sample"
-  )
-
-  metrics <- dplyr::left_join(metrics,
-    eem_fluorescence_index(eem, verbose = FALSE),
-    by = "sample"
-  )
-
-  metrics <- dplyr::left_join(metrics,
-    eem_humification_index(eem, verbose = FALSE),
-    by = "sample"
-  )
-
-  metrics[, -1] <- round(metrics[, -1], digits = 2)
-
-  # nl <- vector(mode = "list", length = length(eem_names(eem)))
-  # names(nl) <- eem_names(eem)
-  # nl[1:length(nl)] <- 1:length(nl)
-
-  ui <- shiny::fluidPage(
-    shiny::titlePanel("EEM interactive visualization"),
-
-    shiny::sidebarLayout(
-      shiny::sidebarPanel
-      (
-        shiny::checkboxInput("scale", label = "Keep z-axis fixed?", FALSE),
-        shiny::hr(),
-        shiny::checkboxInput("by", "Combined 2x2 plots", FALSE),
-        shiny::hr(),
-        shiny::sliderInput("ex_cut", "Select excitation range",
-          min = min(eem[[1]]$ex),
-          max = max(eem[[1]]$ex),
-          value = c(min(eem[[1]]$ex), max(eem[[1]]$ex)),
-          step = 1
-        ),
-        shiny::hr(),
-        shiny::sliderInput("em_cut", "Select emission range",
-          min = min(eem[[1]]$em),
-          max = max(eem[[1]]$em),
-          value = c(min(eem[[1]]$em), max(eem[[1]]$em)),
-          step = 1
-        )
-      ),
-
-
-      shiny::mainPanel(shiny::plotOutput(outputId = "myeem", width = "550px", height = "550px"))
-    ),
-
-    shiny::br(),
-
-    DT::dataTableOutput("eem_list"),
-
-    shiny::br()
-  )
-
-  server <- function(input, output) {
-    output$myeem <- shiny::renderPlot({
-      if (input$scale) {
-        zlim <- range(unlist(lapply(eem, function(x) x$x)), na.rm = TRUE)
-      } else {
-        zlim <- range(eem[[input$eem_list_rows_selected]]$x, na.rm = TRUE)
-      }
-
-      if (!is.null(input$eem_list_rows_selected)) {
-        n <- ifelse(input$by, 2, 1)
-
-        par(mfrow = c(n, n))
-
-        plot(eem,
-          which = input$eem_list_rows_selected,
-          xlim = c(input$ex_cut[1], input$ex_cut[2]),
-          ylim = c(input$em_cut[1], input$em_cut[2]),
-          zlim = zlim
-        )
-      }
-    })
-
-    output$eem_list <- DT::renderDataTable(
-      metrics,
-      server = FALSE,
-      selection = "single",
-      # selection = list(mode = 'single', target = "row", selected = c(1)),
-      options = list(
-        autoWidth = TRUE,
-        columnDefs = list(list(width = "10px", targets = "_all"))
-      )
-    )
-  }
-
-  shiny::shinyApp(ui, server)
-}
-
-
-#' Extract blank EEM
-#'
-#' @template template_eem
-#' @param average Logical. If TRUE blank EEMs will be averaged
-eem_extract_blank <- function(eem, average = TRUE) {
-  blank_names <- c("nano", "miliq", "milliq", "mq", "blank")
-
-  blank <- eem_extract(eem, blank_names,
-    keep = TRUE,
-    ignore_case = TRUE,
-    verbose = FALSE
-  )
-
-  # Average all the blank EEMs
-  if (average) {
-    n <- length(blank)
-
-    message("A total of ", n, " blank EEMs will be averaged.")
-
-    X <- Reduce("+", lapply(blank, function(x) x$x))
-    X <- X / n
-
-    blank <- blank[1]
-    blank[[1]]$x <- X
-
-    class(blank) <- "eemlist"
-  }
-
-  return(blank)
-}
+#' @importFrom graphics par plot text filled.contour title
+#' @importFrom viridis viridis
+.plot_eem <- function(x, show_peaks, ...) {
+  filled.contour(
+    y = x$em,
+    x = x$ex,
+    z = t(x$x),
+    plot.title = title(
+      main = paste(x$sample, "\n", attr(x, "manucafturer"), sep = ""),
+      xlab = "Excitation (nm.)",
+      ylab = "Emission (nm.)"
+    ),
+    key.title = title("Fluorescence\nintensity"),
+    color.palette = viridis::viridis,
+    nlevels = 7,
+    ...
+  )
+  #
+  # fields::image.plot(y = x$em,
+  #              x = x$ex,
+  #              z = t(x$x),
+  #              main = paste(x$sample, "\n", attr(x, "manucafturer"), sep = ""),
+  #              xlab = "Excitation (nm.)",
+  #              ylab = "Emission (nm.)",
+  #              legend.lab = "Fluorescence intensity",
+  #              col = viridis::viridis(256),
+  #              nlevel = 7,
+  #
+  #              ...)
+
+  if (show_peaks) {
+    coble_ex_peak <- list(b = 275, t = 275, a = 260, m = 312, c = 350)
+    coble_em_peak <- list(b = 310, t = 340, a = 420, m = 400, c = 450)
+
+    text(coble_ex_peak$b, coble_em_peak$b, "B", font = 2, cex = 1)
+    text(coble_ex_peak$t, coble_em_peak$t, "T", font = 2, cex = 1)
+    text(coble_ex_peak$a, coble_em_peak$a, "A", font = 2, cex = 1)
+    text(coble_ex_peak$m, coble_em_peak$m, "M", font = 2, cex = 1)
+    text(coble_ex_peak$c, coble_em_peak$c, "C", font = 2, cex = 1)
+  }
+}
+
+#' Surface plot of eem
+#'
+#' @param x An object of class \code{eemlist}.
+#' @param which An integer representing the index of eem to be plotted.
+#' @param ... Extra arguments for \code{image.plot}.
+#' @param show_peaks Boolean indicating if Cobble's peaks should be displayed on
+#'   the surface plot. Default is FALSE.
+#' @param interactive If \code{TRUE} a Shiny app will start to visualize EEMS.
+#'
+#' @export
+#' @examples
+#' folder <- system.file("extdata/cary/scans_day_1/", package = "eemR")
+#' eem <- eem_read(folder, import_function = "cary")
+#'
+#' plot(eem, which = 3)
+plot.eemlist <- function(x, which = 1,
+                         interactive = FALSE, show_peaks = FALSE, ...) {
+  stopifnot(which <= length(x))
+
+  if (interactive) {
+    .plot_shiny(x)
+  } else {
+    .plot_eem(x[[which]], show_peaks, ...)
+  }
+}
+
+eem_as_summary <- function(object) {
+  df <- data.frame(
+    sample = object$sample,
+    ex_min = min(object$ex),
+    ex_max = max(object$ex),
+    em_min = min(object$em),
+    em_max = max(object$em),
+    is_blank_corrected = attr(object, "is_blank_corrected"),
+    is_scatter_corrected = attr(object, "is_scatter_corrected"),
+    is_ife_corrected = attr(object, "is_ife_corrected"),
+    is_raman_normalized = attr(object, "is_raman_normalized")
+  )
+
+  return(df)
+}
+
+#' Display summary of an eemlist object
+#'
+#' @param x An object of class \code{eemlist}.
+#' @param ... Extra arguments.
+#' @template template_summary
+#'
+#' @export
+#' @examples
+#' folder <- system.file("extdata/cary", package = "eemR")
+#' eem <- eem_read(folder, recursive = TRUE, import_function = "cary")
+#'
+#' print(eem)
+print.eemlist <- function(x, ...) {
+  stopifnot(class(x) == "eemlist")
+
+  df <- lapply(x, eem_as_summary)
+  df <- do.call(rbind, df)
+
+  print(df)
+
+  invisible(df)
+}
+
+#' Display summary of an eemlist object
+#'
+#' @param object An object of class \code{eemlist}.
+#' @param ... Extra arguments.
+#' @template template_summary
+#' @export
+#' @examples
+#' folder <- system.file("extdata/cary", package = "eemR")
+#' eem <- eem_read(folder, recursive = TRUE, import_function = "cary")
+#'
+#' summary(eem)
+summary.eemlist <- function(object, ...) {
+  stopifnot(class(object) == "eemlist")
+
+  df <- lapply(object, eem_as_summary)
+  df <- do.call(rbind, df)
+
+  print(df)
+
+  invisible(df)
+}
+
+
+#' Cut emission and/or excitation wavelengths from EEMs
+#'
+#' @template template_eem
+#' @param ex A numeric vector of excitation wavelengths to be removed.
+#' @param em A numeric vector of emission wavelengths to be removed.
+#' @param exact Logical. If TRUE, only wavelengths matching \code{em} and/or
+#'   \code{ex} will be removed. If FALSE, all wavelengths in the range of
+#'   \code{em} and/or \code{ex} will be removed.
+#' @param fill_with_na Logical. If TRUE, fluorescence values at specified
+#'   wavelengths will be replaced with NA. If FALSE, these values will be
+#'   removed.
+#' @export
+#' @examples
+#' # Open the fluorescence eem
+#' file <- system.file("extdata/cary/scans_day_1/", "sample1.csv", package = "eemR")
+#'
+#' eem <- eem_read(file, import_function = "cary")
+#' plot(eem)
+#'
+#' # Cut few excitation wavelengths
+#' eem <- eem_cut(eem, ex = c(220, 225, 230, 230))
+#' plot(eem)
+#'
+#' eem <- eem_read(file, import_function = "cary")
+#' eem <- eem_cut(eem, em = 350:400, fill_with_na = TRUE)
+#' plot(eem)
+eem_cut <- function(eem, ex, em, exact = TRUE, fill_with_na = FALSE) {
+  stopifnot(
+    .is_eemlist(eem) | .is_eem(eem)
+  )
+
+  ## It is a list of eems, then call lapply
+  if (.is_eemlist(eem)) {
+    res <-
+      lapply(
+        eem,
+        eem_cut,
+        ex = ex,
+        em = em,
+        exact = exact,
+        fill_with_na = fill_with_na
+      )
+
+    class(res) <- class(eem)
+
+    return(res)
+  }
+
+  ## Maybe round em and ex wavelengths
+
+  if (!missing(ex)) {
+    stopifnot(
+      is.numeric(ex),
+      all(ex >= 0)
+    )
+
+    if (exact) {
+      index <- which(eem$ex %in% ex)
+    } else {
+      index <- which(is_between(
+        eem$ex,
+        min(ex, na.rm = TRUE),
+        max(ex, na.rm = TRUE)
+      ))
+    }
+
+    if (length(index != 0)) {
+      if (fill_with_na) {
+        # eem$ex[index] <- NA
+        eem$x[, index] <- NA
+      }
+      else {
+        eem$ex <- eem$ex[-index]
+        eem$x <- eem$x[, -index]
+      }
+    }
+  }
+
+  if (!missing(em)) {
+    stopifnot(
+      is.numeric(em),
+      all(em >= 0)
+    )
+
+    if (exact) {
+      index <- which(eem$em %in% em)
+    } else {
+      index <- which(is_between(
+        eem$em,
+        min(em, na.rm = TRUE),
+        max(em, na.rm = TRUE)
+      ))
+    }
+
+    if (length(index != 0)) {
+      if (fill_with_na) {
+        # eem$em[index] <- NA
+        eem$x[index, ] <- NA
+      }
+      else {
+        eem$em <- eem$em[-index]
+        eem$x <- eem$x[-index, ]
+      }
+    }
+  }
+
+  return(eem)
+}
+
+#' Set Excitation and/or Emission wavelengths
+#'
+#' This function allows to manually specify either excitation or emission vector
+#' of wavelengths in EEMs. This function is mostly used with spectrophotometers
+#' such as Shimadzu that do not include excitation wavelengths in fluorescence
+#' files.
+#'
+#' @template template_eem
+#' @param ex A numeric vector of excitation wavelengths.
+#' @param em A numeric vector of emission wavelengths.
+#'
+#' @examples
+#' folder <- system.file("extdata/shimadzu", package = "eemR")
+#'
+#' eem <- eem_read(folder, import_function = "shimadzu")
+#' eem <- eem_set_wavelengths(eem, ex = seq(230, 450, by = 5))
+#'
+#' plot(eem)
+#' @export
+
+eem_set_wavelengths <- function(eem, ex, em) {
+  stopifnot(.is_eemlist(eem) | .is_eem(eem))
+
+  ## It is a list of eems, then call lapply
+  if (.is_eemlist(eem)) {
+    res <- lapply(eem, eem_set_wavelengths, ex = ex, em = em)
+
+    class(res) <- class(eem)
+
+    return(res)
+  }
+
+  if (!missing(ex)) {
+    stopifnot(
+      is.vector(ex),
+      is.numeric(ex),
+      identical(length(ex), ncol(eem$x)),
+      all(ex == cummax(ex))
+    ) ## Monotonously increasing
+
+    eem$ex <- ex
+  }
+
+  if (!missing(em)) {
+    stopifnot(
+      is.vector(em),
+      is.numeric(em),
+      identical(length(em), nrow(eem$x)),
+      all(em == cummax(em))
+    ) ## Monotonously increasing
+
+    eem$em <- em
+  }
+
+  return(eem)
+}
+
+#' Extract EEM samples
+#'
+#' @template template_eem
+#'
+#' @param sample Either numeric of character vector. See \code{details} for more
+#'   information.
+#'
+#' @param keep logical. If TRUE, the specified \code{sample} will be returned.
+#'   If FALSE, they will be removed.
+#'
+#' @param ignore_case Logical, should sample name case should be ignored (TRUE)
+#'   or not (FALSE). Default is FALSE.
+#'
+#' @param verbose Logical determining if removed/extracted eems should be
+#'   printed on screen.
+#'
+#' @details \code{sample} argument can be either numeric or character vector. If
+#'   it is numeric, samples at specified index will be removed.
+#'
+#'   If \code{sample} is character, regular expression will be used and all
+#'   sample names that have a partial or complete match with the expression will
+#'   be removed. See \code{examples} for more details.
+#'
+#' @examples
+#' folder <- system.file("extdata/cary/scans_day_1", package = "eemR")
+#' eems <- eem_read(folder, import_function = "cary")
+#'
+#' eems
+#'
+#' # Remove first and third samples
+#' eem_extract(eems, c(1, 3))
+#'
+#' # Remove everything except first and third samples
+#' eem_extract(eems, c(1, 3), keep = TRUE)
+#'
+#' # Remove all samples containing "3" in their names.
+#' eem_extract(eems, "3")
+#'
+#' # Remove all samples containing either character "s" or character "2" in their names.
+#' eem_extract(eems, c("s", "2"))
+#'
+#' # Remove all samples containing "blank" or "nano"
+#' eem_extract(eems, c("blank", "nano"))
+#' @export
+eem_extract <- function(eem, sample, keep = FALSE, ignore_case = FALSE,
+                        verbose = TRUE) {
+  stopifnot(
+    class(eem) == "eemlist",
+    is.character(sample) | is.numeric(sample)
+  )
+
+  sample_names <- unlist(lapply(eem, function(x) {
+    x$sample
+  }))
+
+  ## Sample number
+  if (is.numeric(sample)) {
+    stopifnot(all(is_between(sample, 1, length(eem))))
+
+    to_remove <- ifelse(rep(keep, length(sample)),
+      setdiff(1:length(eem), sample),
+      sample
+    )
+
+    eem[to_remove] <- NULL
+
+    if (verbose) {
+      cat(
+        ifelse(keep, "Extracted sample(s):", "Removed sample(s):"),
+        sample_names[sample], "\n"
+      )
+    }
+  }
+
+  ## Regular expression
+  if (is.character(sample)) {
+    to_remove <- grepl(paste(sample, collapse = "|"),
+      sample_names,
+      ignore.case = ignore_case
+    )
+
+    eem[xor(to_remove, keep)] <- NULL
+
+    if (verbose) {
+      if (all(to_remove == FALSE)) {
+        cat("Nothing to remove.")
+      }
+      else {
+        cat(
+          ifelse(keep, "Extracted sample(s):", "Removed sample(s):"),
+          sample_names[to_remove], "\n"
+        )
+      }
+    }
+  }
+
+  return(eem)
+}
+
+#' The names of an eem or eemlist objects
+#'
+#' @template template_eem
+#'
+#' @return A character vector containing the names of the EEMs.
+#'
+#' @examples
+#' file <- system.file("extdata/cary/", package = "eemR")
+#' eem <- eem_read(file, recursive = TRUE, import_function = "cary")
+#'
+#' eem_names(eem)
+#' @export
+eem_names <- function(eem) {
+  stopifnot(.is_eemlist(eem) | .is_eem(eem))
+
+  ## It is a list of eems, then call lapply
+  if (.is_eemlist(eem)) {
+    res <- unlist(lapply(eem, eem_names))
+
+    return(res)
+  }
+
+  return(eem$sample)
+}
+
+
+#' Set the sample names of an eem or eemlist objects
+#'
+#' @param x An object of class \code{eem} or \code{eemlist}.
+#' @param value A character vector with new sample names. Must be equal
+#'   in length to the number of samples in the \code{eem} or \code{eemlist}.
+#'
+#' @return An \code{eem} or \code{eemlist}.
+#'
+#' @examples
+#' folder <- system.file("extdata/cary/scans_day_1", package = "eemR")
+#' eems <- eem_read(folder, import_function = "cary")
+#'
+#' eem_names(eems)
+#' eem_names(eems) <- c("a", "b", "c", "d")
+#' eem_names(eems)
+#' @export
+`eem_names<-` <- function(x, value) {
+  stopifnot(.is_eemlist(x) | .is_eem(x))
+
+  if (.is_eemlist(x)) {
+    stopifnot(length(x) == length(value))
+
+    res <- Map(`eem_names<-`, x[], value)
+
+    class(res) <- "eemlist"
+    return(res)
+  }
+
+  stopifnot(length(value) == 1)
+
+  x$sample <- value
+
+  class(x) <- "eem"
+  return(x)
+}
+
+#' Bind eem or eemlist
+#'
+#' Function to bind EEMs that have been loaded from different folders or have
+#' been processed differently.
+#'
+#' @param ... One or more object of class \code{eemlist}.
+#'
+#' @return An object of \code{eemlist}.
+#' @export
+#'
+#' @examples
+#' file <- system.file("extdata/cary/scans_day_1/", "sample1.csv", package = "eemR")
+#' eem <- eem_read(file, import_function = "cary")
+#'
+#' eem <- eem_bind(eem, eem)
+eem_bind <- function(...) {
+  eem <- c(...)
+
+  list_classes <- unlist(lapply(eem, function(x) {
+    class(x)
+  }))
+
+  stopifnot(all(list_classes %in% c("eem", "eemlist")))
+
+  eem <- lapply(eem, my_unlist)
+  eem <- unlist(eem, recursive = FALSE)
+
+  class(eem) <- "eemlist"
+
+  return(eem)
+}
+
+my_unlist <- function(x) {
+  if (class(x) == "eem") {
+    x <- list(x)
+
+    class(x) <- "eemlist"
+
+    return(x)
+  } else {
+    return(x)
+  }
+}
+
+.is_eemlist <- function(eem) {
+  ifelse(class(eem) == "eemlist", TRUE, FALSE)
+}
+
+.is_eem <- function(eem) {
+  ifelse(class(eem) == "eem", TRUE, FALSE)
+}
+
+.plot_shiny <- function(eem) {
+  metrics <- dplyr::left_join(eem_coble_peaks(eem, verbose = FALSE),
+    eem_biological_index(eem, verbose = FALSE),
+    by = "sample"
+  )
+
+  metrics <- dplyr::left_join(metrics,
+    eem_fluorescence_index(eem, verbose = FALSE),
+    by = "sample"
+  )
+
+  metrics <- dplyr::left_join(metrics,
+    eem_humification_index(eem, verbose = FALSE),
+    by = "sample"
+  )
+
+  metrics[, -1] <- round(metrics[, -1], digits = 2)
+
+  # nl <- vector(mode = "list", length = length(eem_names(eem)))
+  # names(nl) <- eem_names(eem)
+  # nl[1:length(nl)] <- 1:length(nl)
+
+  ui <- shiny::fluidPage(
+    shiny::titlePanel("EEM interactive visualization"),
+
+    shiny::sidebarLayout(
+      shiny::sidebarPanel
+      (
+        shiny::checkboxInput("scale", label = "Keep z-axis fixed?", FALSE),
+        shiny::hr(),
+        shiny::checkboxInput("by", "Combined 2x2 plots", FALSE),
+        shiny::hr(),
+        shiny::sliderInput("ex_cut", "Select excitation range",
+          min = min(eem[[1]]$ex),
+          max = max(eem[[1]]$ex),
+          value = c(min(eem[[1]]$ex), max(eem[[1]]$ex)),
+          step = 1
+        ),
+        shiny::hr(),
+        shiny::sliderInput("em_cut", "Select emission range",
+          min = min(eem[[1]]$em),
+          max = max(eem[[1]]$em),
+          value = c(min(eem[[1]]$em), max(eem[[1]]$em)),
+          step = 1
+        )
+      ),
+
+
+      shiny::mainPanel(shiny::plotOutput(outputId = "myeem", width = "550px", height = "550px"))
+    ),
+
+    shiny::br(),
+
+    DT::dataTableOutput("eem_list"),
+
+    shiny::br()
+  )
+
+  server <- function(input, output) {
+    output$myeem <- shiny::renderPlot({
+      if (input$scale) {
+        zlim <- range(unlist(lapply(eem, function(x) x$x)), na.rm = TRUE)
+      } else {
+        zlim <- range(eem[[input$eem_list_rows_selected]]$x, na.rm = TRUE)
+      }
+
+      if (!is.null(input$eem_list_rows_selected)) {
+        n <- ifelse(input$by, 2, 1)
+
+        par(mfrow = c(n, n))
+
+        plot(eem,
+          which = input$eem_list_rows_selected,
+          xlim = c(input$ex_cut[1], input$ex_cut[2]),
+          ylim = c(input$em_cut[1], input$em_cut[2]),
+          zlim = zlim
+        )
+      }
+    })
+
+    output$eem_list <- DT::renderDataTable(
+      metrics,
+      server = FALSE,
+      selection = "single",
+      # selection = list(mode = 'single', target = "row", selected = c(1)),
+      options = list(
+        autoWidth = TRUE,
+        columnDefs = list(list(width = "10px", targets = "_all"))
+      )
+    )
+  }
+
+  shiny::shinyApp(ui, server)
+}
+
+
+#' Extract blank EEM
+#'
+#' @template template_eem
+#' @param average Logical. If TRUE blank EEMs will be averaged
+eem_extract_blank <- function(eem, average = TRUE) {
+  blank_names <- c("nano", "miliq", "milliq", "mq", "blank")
+
+  blank <- eem_extract(eem, blank_names,
+    keep = TRUE,
+    ignore_case = TRUE,
+    verbose = FALSE
+  )
+
+  # Average all the blank EEMs
+  if (average) {
+    n <- length(blank)
+
+    message("A total of ", n, " blank EEMs will be averaged.")
+
+    X <- Reduce("+", lapply(blank, function(x) x$x))
+    X <- X / n
+
+    blank <- blank[1]
+    blank[[1]]$x <- X
+
+    class(blank) <- "eemlist"
+  }
+
+  return(blank)
+}