lint terms

taxonomicallyinformedannotation · Feb 26, 2025 · 0d66cc6 · 0d66cc6
1 parent 8dc67d3
commit 0d66cc6
Show file tree

Hide file tree

Showing 2 changed files with 14 additions and 14 deletions.
diff --git a/R/clean_bio.R b/R/clean_bio.R
@@ -191,25 +191,25 @@ clean_bio <-
       ## In case there are no consensus at all because no network
       tidytable::mutate(tidytable::across(.cols = tidyselect::where(is.logical), .fns = as.character)) |>
       tidytable::mutate(
-        feature_pred_tax_cla_01kin_val = tidytable::coalesce(feature_pred_tax_cla_01kin_val, "dummy"),
+        feature_pred_tax_cla_01kin_val = tidytable::coalesce(feature_pred_tax_cla_01kin_val, "empty"),
         consistency_structure_cla_kin = tidytable::coalesce(consistency_structure_cla_kin, 1),
         feature_pred_tax_cla_01kin_score = tidytable::coalesce(feature_pred_tax_cla_01kin_score, 0),
-        feature_pred_tax_npc_01pat_val = tidytable::coalesce(feature_pred_tax_npc_01pat_val, "dummy"),
+        feature_pred_tax_npc_01pat_val = tidytable::coalesce(feature_pred_tax_npc_01pat_val, "empty"),
         consistency_structure_npc_pat = tidytable::coalesce(consistency_structure_npc_pat, 1),
         feature_pred_tax_npc_01pat_score = tidytable::coalesce(feature_pred_tax_npc_01pat_score, 0),
-        feature_pred_tax_cla_02sup_val = tidytable::coalesce(feature_pred_tax_cla_02sup_val, "dummy"),
+        feature_pred_tax_cla_02sup_val = tidytable::coalesce(feature_pred_tax_cla_02sup_val, "empty"),
         consistency_structure_cla_sup = tidytable::coalesce(consistency_structure_cla_sup, 1),
         feature_pred_tax_cla_02sup_score = tidytable::coalesce(feature_pred_tax_cla_02sup_score, 0),
-        feature_pred_tax_npc_02sup_val = tidytable::coalesce(feature_pred_tax_npc_02sup_val, "dummy"),
+        feature_pred_tax_npc_02sup_val = tidytable::coalesce(feature_pred_tax_npc_02sup_val, "empty"),
         consistency_structure_npc_sup = tidytable::coalesce(consistency_structure_npc_sup, 1),
         feature_pred_tax_npc_02sup_score = tidytable::coalesce(feature_pred_tax_npc_02sup_score, 0),
-        feature_pred_tax_cla_03cla_val = tidytable::coalesce(feature_pred_tax_cla_03cla_val, "dummy"),
+        feature_pred_tax_cla_03cla_val = tidytable::coalesce(feature_pred_tax_cla_03cla_val, "empty"),
         consistency_structure_cla_cla = tidytable::coalesce(consistency_structure_cla_cla, 1),
         feature_pred_tax_cla_03cla_score = tidytable::coalesce(feature_pred_tax_cla_03cla_score, 0),
-        feature_pred_tax_npc_03cla_val = tidytable::coalesce(feature_pred_tax_npc_03cla_val, "dummy"),
+        feature_pred_tax_npc_03cla_val = tidytable::coalesce(feature_pred_tax_npc_03cla_val, "empty"),
         consistency_structure_npc_cla = tidytable::coalesce(consistency_structure_npc_cla, 1),
         feature_pred_tax_npc_03cla_score = tidytable::coalesce(feature_pred_tax_npc_03cla_score, 0),
-        feature_pred_tax_cla_04dirpar_val = tidytable::coalesce(feature_pred_tax_cla_04dirpar_val, "dummy"),
+        feature_pred_tax_cla_04dirpar_val = tidytable::coalesce(feature_pred_tax_cla_04dirpar_val, "empty"),
         consistency_structure_cla_par = tidytable::coalesce(consistency_structure_cla_par, 1),
         feature_pred_tax_cla_04dirpar_score = tidytable::coalesce(feature_pred_tax_cla_04dirpar_score, 0)
       )

diff --git a/R/decorate_chemo.R b/R/decorate_chemo.R
@@ -36,49 +36,49 @@ decorate_chemo <- function(annot_table_wei_chemo =
     tidytable::filter(
       feature_pred_tax_cla_01kin_val != "notAnnotated" &
         feature_pred_tax_cla_01kin_val != "notConsistent" &
-        feature_pred_tax_cla_01kin_val != "dummy"
+        feature_pred_tax_cla_01kin_val != "empty"
     )
   df_npc_pat <- annot_table_wei_chemo |>
     tidytable::filter(score_chemical >= score_chemical_npc_pathway * 1) |>
     tidytable::filter(
       feature_pred_tax_npc_01pat_val != "notAnnotated" &
         feature_pred_tax_npc_01pat_val != "notConsistent" &
-        feature_pred_tax_npc_01pat_val != "dummy"
+        feature_pred_tax_npc_01pat_val != "empty"
     )
   df_cla_sup <- df_cla_kin |>
     tidytable::filter(score_chemical >= score_chemical_cla_superclass * 1) |>
     tidytable::filter(
       feature_pred_tax_cla_02sup_val != "notAnnotated" &
         feature_pred_tax_cla_02sup_val != "notConsistent" &
-        feature_pred_tax_cla_02sup_val != "dummy"
+        feature_pred_tax_cla_02sup_val != "empty"
     )
   df_npc_sup <- df_npc_pat |>
     tidytable::filter(score_chemical >= score_chemical_npc_superclass * 1) |>
     tidytable::filter(
       feature_pred_tax_npc_02sup_val != "notAnnotated" &
         feature_pred_tax_npc_02sup_val != "notConsistent" &
-        feature_pred_tax_npc_02sup_val != "dummy"
+        feature_pred_tax_npc_02sup_val != "empty"
     )
   df_cla_cla <- df_cla_sup |>
     tidytable::filter(score_chemical >= score_chemical_cla_class * 1) |>
     tidytable::filter(
       feature_pred_tax_cla_03cla_val != "notAnnotated" &
         feature_pred_tax_cla_03cla_val != "notConsistent" &
-        feature_pred_tax_cla_03cla_val != "dummy"
+        feature_pred_tax_cla_03cla_val != "empty"
     )
   df_npc_cla <- df_npc_sup |>
     tidytable::filter(score_chemical >= score_chemical_npc_class * 1) |>
     tidytable::filter(
       feature_pred_tax_npc_03cla_val != "notAnnotated" &
         feature_pred_tax_npc_03cla_val != "notConsistent" &
-        feature_pred_tax_npc_03cla_val != "dummy"
+        feature_pred_tax_npc_03cla_val != "empty"
     )
   df_cla_par <- df_cla_cla |>
     tidytable::filter(score_chemical >= score_chemical_cla_parent * 1) |>
     tidytable::filter(
       feature_pred_tax_cla_04dirpar_val != "notAnnotated" &
         feature_pred_tax_cla_04dirpar_val != "notConsistent" &
-        feature_pred_tax_cla_04dirpar_val != "dummy"
+        feature_pred_tax_cla_04dirpar_val != "empty"
     )
 
   log_debug(