fix

taxonomicallyinformedannotation · Jul 22, 2023 · 44c283f · 44c283f
1 parent 481b161
commit 44c283f
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Showing 6 changed files with 141 additions and 96 deletions.
diff --git a/R/create_edges_parallel.R b/R/create_edges_parallel.R
@@ -23,8 +23,9 @@ create_edges_parallel <- function(index,
     FUN = create_edges_progress,
     query = index,
     s1 = cbind(mz = frags[[index]][, 1], intensity = frags[[index]][, 2]),
-    fragments = frags,
-    precursors = precs
-  )
+    frags = frags,
+    precs = precs
+  ) |>
+    tidytable::bind_rows()
   return(list)
 }
diff --git a/R/create_edges_progress.R b/R/create_edges_progress.R
@@ -1,3 +1,5 @@
+library(MsCoreUtils)
+
 utils::globalVariables(
   c(
     "params"
@@ -12,8 +14,8 @@ utils::globalVariables(
 #' @param target Indices of target spectra
 #' @param query Index of query spectra
 #' @param s1 Query spectrum
-#' @param fragments Fragments
-#' @param precursors Precursors
+#' @param frags Fragments
+#' @param precs Precursors
 #'
 #' @return NULL
 #'
@@ -23,30 +25,28 @@ utils::globalVariables(
 create_edges_progress <- function(target,
                                   query,
                                   s1,
-                                  fragments,
-                                  precursors) {
+                                  frags,
+                                  precs) {
   s2 <-
-    cbind(mz = fragments[[target]][, 1], intensity = fragments[[target]][, 2])
+    cbind(mz = frags[[target]][, 1], intensity = frags[[target]][, 2])
   map <-
-    MsCoreUtils::join_gnps(
+    join_gnps(
       x = s1[, 1],
       y = s2[, 1],
-      xPrecursorMz = precursors[query],
-      yPrecursorMz = precursors[target],
+      xPrecursorMz = precs[query],
+      yPrecursorMz = precs[target],
       tolerance = params$ms$tolerances$mass$dalton$ms2,
       ppm = params$ms$tolerances$mass$ppm$ms2
     )
-  score <- MsCoreUtils::gnps(s1[map$x, ], s2[map$y, ])
-  matched_peaks_count <-
-    length((map$x * map$y)[!is.na(map$x * map$y)])
-  presence_ratio <- matched_peaks_count / length(map$y)
-  return(
-    data.frame(
-      "feature_id" = query,
-      "target_id" = target,
-      "score" = score,
-      "matched_peaks_count" = matched_peaks_count,
-      "presence_ratio" = presence_ratio
+  matched_peaks_count <- length((map$x * map$y)[!is.na(map$x * map$y)])
+  presence_ratio <-
+    return(
+      data.frame(
+        "feature_id" = query,
+        "target_id" = target,
+        "score" = gnps(s1[map$x, ], s2[map$y, ]),
+        "matched_peaks_count" = matched_peaks_count,
+        "presence_ratio" = matched_peaks_count / length(map$y)
+      )
     )
-  )
 }
diff --git a/R/create_edges_spectra.R b/R/create_edges_spectra.R
@@ -83,31 +83,26 @@ create_edges_spectra <- function(
       Spectra::addProcessing(normalize_peaks()) |>
       Spectra::applyProcessing()
 
-    log_debug("Extracting fragments and precursors...")
-    fragments_norm <- spectra@backend@peaksData
-    precursors <- spectra$precursorMz
-    nspe <- length(spectra)
-
     log_debug("Performing spectral comparison")
     log_debug(
       "As we do not bin the spectra,
       nor limit the precursors delta,
       expect a long processing time."
     )
     log_debug("Take yourself a break, you deserve it.")
-
+    nspecz <- length(spectra)
+    precz <- spectra$precursorMz
+    fragz <- spectra@backend@peaksData
     ## Originally written with future but too slow...TODO investigate
-    matches_sim <- pbmcapply::pbmclapply(
-      X = 1:(nspe - 1),
+    edges <- pbmcapply::pbmclapply(
+      X = 1:(nspecz - 1),
       mc.cores = parallelly::availableCores(),
       ignore.interactive = TRUE,
       FUN = create_edges_parallel,
-      frags = fragments_norm,
-      precs = precursors,
-      nspecs = nspe
-    )
-
-    edges <- matches_sim |>
+      frags = fragz,
+      precs = precz,
+      nspecs = nspecz
+    ) |>
       tidytable::bind_rows()
 
     ## old version, keep in case