Merge pull request #154 from taxonomicallyinformedannotation/dev

Dev
taxonomicallyinformedannotation · Jul 5, 2024 · b48bf51 · b48bf51
2 parents 4bbc2c8 + d6bf4e6
commit b48bf51
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Showing 3 changed files with 28 additions and 9 deletions.
diff --git a/R/prepare_libraries_rt.R b/R/prepare_libraries_rt.R
@@ -69,6 +69,24 @@ prepare_libraries_rt <-
         !is.null(x)
       }) |>
       unlist()]
+    mgf_exp <- mgf_exp |>
+      lapply(
+        FUN = full_or_null
+      )
+    temp_exp <- temp_exp[temp_exp |>
+      lapply(FUN = function(x) {
+        !is.null(x)
+      }) |>
+      unlist()]
+    mgf_is <- mgf_is |>
+      lapply(
+        FUN = full_or_null
+      )
+    temp_is <- temp_is[temp_is |>
+      lapply(FUN = function(x) {
+        !is.null(x)
+      }) |>
+      unlist()]
     if (length(mgf_exp) == 0) {
       mgf_exp <- NULL
     }
@@ -300,7 +318,7 @@ prepare_libraries_rt <-
     rm(df_rts)
 
     if (nrow(rts) == 0) {
-      log_debug("No retention time library found, returning empty table.")
+      log_debug("No retention time library found, returning empty organism table.")
       sop <- tidytable::tidytable(
         structure_smiles = NA_character_,
         structure_inchikey = NA_character_,
@@ -310,7 +328,7 @@ prepare_libraries_rt <-
     }
 
     if (nrow(rts) == 0) {
-      log_debug("No retention time library found, returning empty tables")
+      log_debug("No retention time library found, returning empty retention time table.")
       rts <- tidytable::tidytable(
         rt = NA_real_,
         candidate_structure_inchikey_no_stereo = NA_character_,

diff --git a/R/prepare_params.R b/R/prepare_params.R
@@ -29,7 +29,8 @@ prepare_params <- function(params_small = get_params(step = "prepare_params"),
   ann_thr_ms1_bio <- params_advanced$annotations$thresholds$ms1$biological
   ann_thr_ms1_che <- params_advanced$annotations$thresholds$ms1$chemical
   ann_thr_ms1_con <- params_advanced$annotations$thresholds$ms1$condition
-  ann_thr_ms2_sim <- params_advanced$annotations$thresholds$ms2$similarity
+  ann_thr_ms2_sim_ann <- params_advanced$annotations$thresholds$ms2$similarity$annotation
+  ann_thr_ms2_sim_edg <- params_advanced$annotations$thresholds$ms2$similarity$edges
   fil_pat <- params_advanced$files$pattern
   fil_ann_raw_spe <- params_advanced$files$annotations$raw$spectral
   fil_ann_raw_spe_gnp <- params_advanced$files$annotations$raw$spectral$gnps
@@ -245,8 +246,8 @@ prepare_params <- function(params_small = get_params(step = "prepare_params"),
     annotate_spectra = {
       yamls_params$annotate_spectra$annotations$ms2approx <-
         ann_ms2_app
-      yamls_params$annotate_spectra$annotations$thresholds$ms2$similarity <-
-        ann_thr_ms2_sim
+      yamls_params$annotate_spectra$annotations$thresholds$ms2$similarity$annotation <-
+        ann_thr_ms2_sim_ann
       yamls_params$annotate_spectra$files$annotations$raw$spectral$spectral <-
         fil_ann_raw_spe_spe
       yamls_params$annotate_spectra$files$libraries$spectral$exp$neg <-
@@ -275,8 +276,8 @@ prepare_params <- function(params_small = get_params(step = "prepare_params"),
         fil_net_spe_com_raw
     },
     create_edges_spectra = {
-      yamls_params$create_edges_spectra$annotations$thresholds$ms2$similarity <-
-        ann_thr_ms2_sim
+      yamls_params$create_edges_spectra$annotations$thresholds$ms2$similarity$edges <-
+        ann_thr_ms2_sim_edg
       yamls_params$create_edges_spectra$files$networks$spectral$edges$raw$spectral <-
         fil_net_spe_edg_raw_spe
       yamls_params$create_edges_spectra$files$spectral$raw <-

diff --git a/inst/params/default/prepare_libraries_rt.yaml b/inst/params/default/prepare_libraries_rt.yaml
@@ -15,7 +15,7 @@ files:
       #' List of experimental temporal libraries.
       exp:
         #' List of experimental temporal libraries (CSV). STRING
-        csv: ~
+        csv: [ ]
 
         #' List of experimental temporal libraries (MGF).
         mgf:
@@ -28,7 +28,7 @@ files:
       #' List of in silico temporal libraries.
       is:
         #' List of in silico temporal libraries (CSV). STRING
-        csv: ~
+        csv: [ ]
 
         #' List of in silico temporal libraries (MGF).
         mgf: