New function eem_peaks() to extract user-defined fluorescence peaks (#42

)

DESCRIPTION

@@ -3,7 +3,7 @@ Type: Package
 Title: Tools for Pre-Processing Emission-Excitation-Matrix (EEM) Fluorescence
     Data
 Version: 0.1.5.9000
-Date: 2017-05-08
+Date: 2018-03-29
 Authors@R: person("Philippe", "Massicotte", email = "pmassicotte@hotmail.com",
   role = c("aut", "cre"))
 Description: Provides various tools for preprocessing Emission-Excitation-Matrix (EEM) for Parallel Factor Analysis (PARAFAC). Different
@@ -22,7 +22,9 @@ Imports:
     readr,
     stats,
     rlist,
-    viridis
+    viridis,
+    purrr,
+    assertthat
 RoxygenNote: 6.0.1
 Suggests:
     cdom,

NAMESPACE

@@ -15,16 +15,19 @@ export(eem_fluorescence_index)
 export(eem_humification_index)
 export(eem_inner_filter_effect)
 export(eem_names)
+export(eem_peaks)
 export(eem_raman_normalisation)
 export(eem_read)
 export(eem_remove_blank)
 export(eem_remove_scattering)
 export(eem_set_wavelengths)
+import(assertthat)
 importFrom(graphics,filled.contour)
 importFrom(graphics,par)
 importFrom(graphics,plot)
 importFrom(graphics,text)
 importFrom(graphics,title)
+importFrom(purrr,map2)
 importFrom(readr,read_lines)
 importFrom(rlist,list.apply)
 importFrom(rlist,list.group)

NEWS.md

@@ -1,5 +1,7 @@
 # eemR 0.1.6 (Unreleased)
 
+ - New function `eem_peaks()` to extract user-defined fluorescence peaks (#42).
+
  - `eem_read()` will try to import unknown file format if it fails to determine it. At the moment the heuristic is not perfect, so the file must be "easy" to read (i.e. contain a square matrix of data).
 
 # eemR 0.1.5

R/eem_metrics.R

@@ -135,6 +135,63 @@ eem_coble_peaks <- function(eem, verbose = TRUE){
                     stringsAsFactors = FALSE))
 }
 
+#' Extract fluorescence peaks
+#'
+#' @param ex A numeric vector with excitation wavelengths.
+#' @param em A numeric vector with emission wavelengths.
+#'
+#' @template template_eem
+#'
+#' @template template_section_interp2
+#'
+#' @return A data frame containing excitation and emission peak values. See
+#'   details for more information.
+#'
+#' @importFrom purrr map2
+#' @import assertthat
+#'
+#' @examples
+#' file <- system.file("extdata/cary/scans_day_1/", "sample1.csv", package = "eemR")
+#' eem <- eem_read(file)
+#'
+#' eem_peaks(eem, ex = c(250, 350), em = c(300, 400))
+#'
+#' @export
+eem_peaks <- function(eem, ex, em, verbose = TRUE) {
+  stopifnot(.is_eemlist(eem) | .is_eem(eem))
+  stopifnot(
+    is.numeric(ex),
+    is.numeric(em),
+    length(ex) == length(em),
+    all(ex > 0),
+    all(em > 0)
+  )
+
+  ## It is a list of eems, then call lapply
+  if (.is_eemlist(eem)) {
+    res <- lapply(eem, eem_peaks, ex, em, verbose = verbose)
+    res <- dplyr::bind_rows(res)
+
+    return(res)
+  }
+
+  assertthat::assert_that(all(dplyr::between(ex, range(eem$ex)[1], range(eem$ex)[2])), msg = "Excitation values are not within the range of excitation values of the EEM.")
+  assertthat::assert_that(all(dplyr::between(em, range(eem$em)[1], range(eem$em)[2])), msg = "Emission values are not within the range of emission values of the EEM.")
+
+  peak_intensity <- purrr::map2(ex, em, function(ex, em) {
+    pracma::interp2(eem$ex, eem$em, eem$x, ex, em)
+  })
+
+  peak_intensity <- unlist(peak_intensity)
+
+  return(data.frame(
+    sample = eem$sample,
+    ex = ex,
+    em = em,
+    peak_intensity = peak_intensity
+  ))
+}
+
 #' Calculate the fluorescence humification index (HIX)
 #'
 #' @template template_eem