add default spectra naming in the process_spectra()

this fixes #37 by evaluating the uniqueness of names before assigning and giving clues on how to make them unique Further tests to downstream functions as `get_spectra_names()` does not allow empty peaks
ClavelLab · Dec 4, 2023 · 8d6484e · 8d6484e
1 parent f445409
commit 8d6484e
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Showing 8 changed files with 131 additions and 39 deletions.
diff --git a/R/get_spectra_names.R b/R/get_spectra_names.R
@@ -36,7 +36,21 @@ get_spectra_names <- function(spectra_list){
       )
     }
 
-    spectra_names <- lapply(spectra_list, function(spectra) {
+    # Need to make sure that the spectra are not empty here to avoid
+    # a tibble issue like:
+    # Error in `tibble::as_tibble_row()`:
+    # ! Columns 1, 2, and 3 must be named.
+    #
+    # Therefore, error if the spectra is empty or not
+    empty_spectra <- vapply(spectra_list, MALDIquant::isEmpty, FUN.VALUE = logical(1))
+
+    if(any(empty_spectra)){
+      stop(
+        "Empty spectra detected! Preprocess the data accordingly using `check_spectra()`"
+      )
+    }
+
+    spectra_names <- lapply(spectra_list,  function(spectra){
       MALDIquant::metaData(spectra)[c("name", "fullName", "file")] %>%
         tibble::as_tibble_row()
     }) %>%
@@ -46,7 +60,7 @@ get_spectra_names <- function(spectra_list){
       ) %>% 
       dplyr::relocate("sanitized_name")
 
-    if( nrow(spectra_names) > dplyr::n_distinct(spectra_names$sanitized_name)){
+    if( nrow(spectra_names) > dplyr::n_distinct(spectra_names[["sanitized_name"]])){
       warning(
         "Non-unique values in spectra names!",
         "\n\nQuickfix: use `dplyr::mutate(sanitized_name = base::make.unique(sanitized_name))`"

diff --git a/R/process_spectra.R b/R/process_spectra.R
@@ -15,6 +15,7 @@
 #'
 #'
 #' @param spectra_list A list of [MALDIquant::MassSpectrum] objects.
+#' @param spectra_names A [tibble::tibble] (or [data.frame]) of sanitized spectra names by default from [get_spectra_names]. If provided manually, the column `sanitized_name` will be used to name the spectra.
 #' @param rds_prefix A character indicating the prefix for the `.RDS` output files to be written in the `processed` directory. By default, no prefix are given and thus no files are written.
 #'
 #' @return A named list of three objects:
@@ -45,7 +46,9 @@
 #' # A detailed view of the metadata with the median signal-to-noise
 #' #  ratio (SNR) and the number of peaks
 #' processed$metadata
-process_spectra <- function(spectra_list, rds_prefix = NULL) {
+process_spectra <- function(spectra_list,
+                            spectra_names = get_spectra_names(spectra_list),
+                            rds_prefix = NULL) {
   # It returns the list and write it for future processing as an RDS file.
 
   # 1. SQRT transformation
@@ -81,15 +84,15 @@ process_spectra <- function(spectra_list, rds_prefix = NULL) {
     "peaks" = lengths(snr_list)
   )
 
-
   # Add the spectra identifiers to all objects
-  rownames(metadata) <- names(spectra) <- names(peaks) <- sapply(spectra, function(x) {
-    # e.g., 230117_1750_1_B1
-    gsub(
-      "[-\\.]", "_",
-      MALDIquant::metaData(x)[["fullName"]]
+  if(! "sanitized_name" %in% colnames(spectra_names)){
+    stop(
+      "Missing 'sanitized_name' column in the provided 'spectra_names' tibble!",
+      "\n\nTip: Use the `get_spectra_names()` for default and compliant names."
     )
-  })
+  }
+  rownames(metadata) <- names(spectra) <- names(peaks) <- spectra_names[["sanitized_name"]]
+
   # Aggregate the objects to a list
   processed_list <- list(
     "spectra" = spectra,

diff --git a/dev/dereplicate-spectra.Rmd b/dev/dereplicate-spectra.Rmd
@@ -56,6 +56,7 @@ The full procedure is illustrated in the example below. While in this case, all
 #'
 #'
 #' @param spectra_list A list of [MALDIquant::MassSpectrum] objects.
+#' @param spectra_names A [tibble::tibble] (or [data.frame]) of sanitized spectra names by default from [get_spectra_names]. If provided manually, the column `sanitized_name` will be used to name the spectra.
 #' @param rds_prefix A character indicating the prefix for the `.RDS` output files to be written in the `processed` directory. By default, no prefix are given and thus no files are written.
 #'
 #' @return A named list of three objects:
@@ -70,7 +71,9 @@ The full procedure is illustrated in the example below. While in this case, all
 #'
 #' @note The original R code on which this function is based is accessible at: <https://github.com/strejcem/MALDIvs16S>
 #' @examples
-process_spectra <- function(spectra_list, rds_prefix = NULL) {
+process_spectra <- function(spectra_list,
+                            spectra_names = get_spectra_names(spectra_list),
+                            rds_prefix = NULL) {
   # It returns the list and write it for future processing as an RDS file.
 
   # 1. SQRT transformation
@@ -106,15 +109,15 @@ process_spectra <- function(spectra_list, rds_prefix = NULL) {
     "peaks" = lengths(snr_list)
   )
 
-
   # Add the spectra identifiers to all objects
-  rownames(metadata) <- names(spectra) <- names(peaks) <- sapply(spectra, function(x) {
-    # e.g., 230117_1750_1_B1
-    gsub(
-      "[-\\.]", "_",
-      MALDIquant::metaData(x)[["fullName"]]
+  if(! "sanitized_name" %in% colnames(spectra_names)){
+    stop(
+      "Missing 'sanitized_name' column in the provided 'spectra_names' tibble!",
+      "\n\nTip: Use the `get_spectra_names()` for default and compliant names."
     )
-  })
+  }
+  rownames(metadata) <- names(spectra) <- names(peaks) <- spectra_names[["sanitized_name"]]
+  
   # Aggregate the objects to a list
   processed_list <- list(
     "spectra" = spectra,
@@ -173,12 +176,32 @@ test_that("process_spectra works", {
     )
   )
 })
-test_that("process_spectra warns on empty spectra", {
-  expect_warning(
+test_that("process_spectra with automatic names fails on empty spectra with maldipickr functions", {
+  expect_error(
     process_spectra(c(MALDIquant::createMassSpectrum(0, 0))),
+    "Empty spectra detected!"
+  )
+})
+test_that("process_spectra with manual names warns on empty spectra with MALDIquant functions", {
+  expect_warning(
+    process_spectra(
+      c(MALDIquant::createMassSpectrum(0, 0)),
+      spectra_names = tibble::tibble(sanitized_name = "Dummy_name")
+    ),
     "MassSpectrum object is empty"
   )
 })
+test_that("process_spectra with manual names fails if wrong column", {
+  expect_error(
+    process_spectra(
+      spectra_list_test,
+      spectra_names = tibble::tibble(
+        sanitized_wrong_column = c("spectra1","spectra2")
+        )
+    ),
+    "Missing 'sanitized_name' column"
+  )
+})
 ```
 
 ## Merge multiple processed spectra
@@ -354,13 +377,13 @@ test_that("merge_processed_spectra fails with the wrong input", {
 
 test_that("merge_processed_spectra fails with only empty peaks", {
   expect_warning(
-    empty_peaks <- list(
-      createMassSpectrum(
-        mass = 4500:5000,
-        intensity = rep(0, 501),
-        metaData = list(fullName = "foo")
-      )
-    ) %>% process_spectra(),
+      empty_peaks <- list(
+        createMassSpectrum(
+          mass = 4500:5000,
+          intensity = rep(0, 501),
+          metaData = list(fullName = "foo")
+        )
+      ) %>% process_spectra(spectra_names = tibble::tibble(sanitized_name = "foo")),
     "MassSpectrum object is empty!"
   )
   expect_warning(

diff --git a/dev/flat_utils.Rmd b/dev/flat_utils.Rmd
@@ -361,7 +361,21 @@ get_spectra_names <- function(spectra_list){
       )
     }
     
-    spectra_names <- lapply(spectra_list, function(spectra) {
+    # Need to make sure that the spectra are not empty here to avoid
+    # a tibble issue like:
+    # Error in `tibble::as_tibble_row()`:
+    # ! Columns 1, 2, and 3 must be named.
+    #
+    # Therefore, error if the spectra is empty or not
+    empty_spectra <- vapply(spectra_list, MALDIquant::isEmpty, FUN.VALUE = logical(1))
+    
+    if(any(empty_spectra)){
+      stop(
+        "Empty spectra detected! Preprocess the data accordingly using `check_spectra()`"
+      )
+    }
+    
+    spectra_names <- lapply(spectra_list,  function(spectra){
       MALDIquant::metaData(spectra)[c("name", "fullName", "file")] %>%
         tibble::as_tibble_row()
     }) %>%
@@ -371,7 +385,7 @@ get_spectra_names <- function(spectra_list){
       ) %>% 
       dplyr::relocate("sanitized_name")
     
-    if( nrow(spectra_names) > dplyr::n_distinct(spectra_names$sanitized_name)){
+    if( nrow(spectra_names) > dplyr::n_distinct(spectra_names[["sanitized_name"]])){
       warning(
         "Non-unique values in spectra names!",
         "\n\nQuickfix: use `dplyr::mutate(sanitized_name = base::make.unique(sanitized_name))`"
@@ -422,6 +436,12 @@ test_that("get_spectra_names warns when duplicate", {
     out$sanitized_name, c("species1_G2", "species1_G2")
   )
 })
+test_that("get_spectra_names fails on empty spectra", {
+  expect_error(
+    get_spectra_names(c(MALDIquant::createMassSpectrum(0, 0))),
+    "Empty spectra detected!"
+  )
+})
 ```
 
 

diff --git a/man/process_spectra.Rd b/man/process_spectra.Rd
diff --git a/tests/testthat/test-get_spectra_names.R b/tests/testthat/test-get_spectra_names.R
@@ -25,3 +25,9 @@ test_that("get_spectra_names warns when duplicate", {
     out$sanitized_name, c("species1_G2", "species1_G2")
   )
 })
+test_that("get_spectra_names fails on empty spectra", {
+  expect_error(
+    get_spectra_names(c(MALDIquant::createMassSpectrum(0, 0))),
+    "Empty spectra detected!"
+  )
+})
diff --git a/tests/testthat/test-merge_processed_spectra.R b/tests/testthat/test-merge_processed_spectra.R
@@ -41,13 +41,13 @@ test_that("merge_processed_spectra fails with the wrong input", {
 
 test_that("merge_processed_spectra fails with only empty peaks", {
   expect_warning(
-    empty_peaks <- list(
-      createMassSpectrum(
-        mass = 4500:5000,
-        intensity = rep(0, 501),
-        metaData = list(fullName = "foo")
-      )
-    ) %>% process_spectra(),
+      empty_peaks <- list(
+        createMassSpectrum(
+          mass = 4500:5000,
+          intensity = rep(0, 501),
+          metaData = list(fullName = "foo")
+        )
+      ) %>% process_spectra(spectra_names = tibble::tibble(sanitized_name = "foo")),
     "MassSpectrum object is empty!"
   )
   expect_warning(

diff --git a/tests/testthat/test-process_spectra.R b/tests/testthat/test-process_spectra.R
@@ -16,9 +16,29 @@ test_that("process_spectra works", {
     )
   )
 })
-test_that("process_spectra warns on empty spectra", {
-  expect_warning(
+test_that("process_spectra with automatic names fails on empty spectra with maldipickr functions", {
+  expect_error(
     process_spectra(c(MALDIquant::createMassSpectrum(0, 0))),
+    "Empty spectra detected!"
+  )
+})
+test_that("process_spectra with manual names warns on empty spectra with MALDIquant functions", {
+  expect_warning(
+    process_spectra(
+      c(MALDIquant::createMassSpectrum(0, 0)),
+      spectra_names = tibble::tibble(sanitized_name = "Dummy_name")
+    ),
     "MassSpectrum object is empty"
   )
 })
+test_that("process_spectra with manual names fails if wrong column", {
+  expect_error(
+    process_spectra(
+      spectra_list_test,
+      spectra_names = tibble::tibble(
+        sanitized_wrong_column = c("spectra1","spectra2")
+        )
+    ),
+    "Missing 'sanitized_name' column"
+  )
+})