From 0d66cc6101b5888d9f61d71bdec52f1ab9efb0d6 Mon Sep 17 00:00:00 2001 From: Adriano Rutz Date: Wed, 26 Feb 2025 13:02:47 +0100 Subject: [PATCH] lint terms --- R/clean_bio.R | 14 +++++++------- R/decorate_chemo.R | 14 +++++++------- 2 files changed, 14 insertions(+), 14 deletions(-) diff --git a/R/clean_bio.R b/R/clean_bio.R index 155386de..408f82ea 100644 --- 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 index 30467b3b..52052e8f 100644 --- 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(