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decorate_chemo.R
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decorate_chemo.R
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import::from(crayon, blue, .into = environment())
import::from(crayon, cyan, .into = environment())
import::from(crayon, green, .into = environment())
import::from(crayon, magenta, .into = environment())
import::from(crayon, red, .into = environment())
import::from(crayon, silver, .into = environment())
import::from(crayon, yellow, .into = environment())
import::from(tidytable, distinct, .into = environment())
import::from(tidytable, filter, .into = environment())
#' @title Decorate chemo
#'
#' @description This function outputs information about chemical weighting
#'
#' @importFrom crayon blue
#' @importFrom crayon cyan
#' @importFrom crayon green
#' @importFrom crayon magenta
#' @importFrom crayon red
#' @importFrom crayon silver
#' @importFrom crayon yellow
#' @importFrom tidytable distinct
#' @importFrom tidytable filter
#'
#' @param annot_table_wei_chemo Table to decorate
#' @param score_chemical_cla_kingdom Classyfire kingdom score
#' @param score_chemical_cla_superclass Classyfire superclass score
#' @param score_chemical_cla_class Classyfire class score
#' @param score_chemical_cla_parent Classyfire parent score
#' @param score_chemical_npc_pathway NPC pathway score
#' @param score_chemical_npc_superclass NPC superclass score
#' @param score_chemical_npc_class NPC class score
#'
#' @return Message indicating the number of annotations
#' weighted at each chemical level
#'
#' @export
#'
#' @examples NULL
decorate_chemo <- function(annot_table_wei_chemo =
get("annot_table_wei_chemo", envir = parent.frame()),
score_chemical_cla_kingdom =
get("score_chemical_cla_kingdom", envir = parent.frame()),
score_chemical_cla_superclass =
get("score_chemical_cla_superclass", envir = parent.frame()),
score_chemical_cla_class =
get("score_chemical_cla_class", envir = parent.frame()),
score_chemical_cla_parent =
get("score_chemical_cla_parent", envir = parent.frame()),
score_chemical_npc_pathway =
get("score_chemical_npc_pathway", envir = parent.frame()),
score_chemical_npc_superclass =
get("score_chemical_npc_superclass", envir = parent.frame()),
score_chemical_npc_class =
get("score_chemical_npc_class", envir = parent.frame())) {
df_cla_kin <- annot_table_wei_chemo |>
filter(score_chemical >= score_chemical_cla_kingdom * 1) |>
filter(
feature_pred_tax_cla_01kin_val != "notAnnotated" &
feature_pred_tax_cla_01kin_val != "notConsistent" &
feature_pred_tax_cla_01kin_val != "dummy"
)
df_npc_pat <- annot_table_wei_chemo |>
filter(score_chemical >= score_chemical_npc_pathway * 1) |>
filter(
feature_pred_tax_npc_01pat_val != "notAnnotated" &
feature_pred_tax_npc_01pat_val != "notConsistent" &
feature_pred_tax_npc_01pat_val != "dummy"
)
df_cla_sup <- df_cla_kin |>
filter(score_chemical >= score_chemical_cla_superclass * 1) |>
filter(
feature_pred_tax_cla_02sup_val != "notAnnotated" &
feature_pred_tax_cla_02sup_val != "notConsistent" &
feature_pred_tax_cla_02sup_val != "dummy"
)
df_npc_sup <- df_npc_pat |>
filter(score_chemical >= score_chemical_npc_superclass * 1) |>
filter(
feature_pred_tax_npc_02sup_val != "notAnnotated" &
feature_pred_tax_npc_02sup_val != "notConsistent" &
feature_pred_tax_npc_02sup_val != "dummy"
)
df_cla_cla <- df_cla_sup |>
filter(score_chemical >= score_chemical_cla_class * 1) |>
filter(
feature_pred_tax_cla_03cla_val != "notAnnotated" &
feature_pred_tax_cla_03cla_val != "notConsistent" &
feature_pred_tax_cla_03cla_val != "dummy"
)
df_npc_cla <- df_npc_sup |>
filter(score_chemical >= score_chemical_npc_class * 1) |>
filter(
feature_pred_tax_npc_03cla_val != "notAnnotated" &
feature_pred_tax_npc_03cla_val != "notConsistent" &
feature_pred_tax_npc_03cla_val != "dummy"
)
df_cla_par <- df_cla_cla |>
filter(score_chemical >= score_chemical_cla_parent * 1) |>
filter(
feature_pred_tax_cla_04dirpar_val != "notAnnotated" &
feature_pred_tax_cla_04dirpar_val != "notConsistent" &
feature_pred_tax_cla_04dirpar_val != "dummy"
)
log_debug(
x = paste(
"chemically informed scoring led to \n",
silver(nrow(
df_cla_kin |>
distinct(candidate_structure_inchikey_no_stereo)
)),
"annotations reranked at the",
silver("(classyfire) kingdom"),
"level, \n",
cyan(nrow(
df_npc_pat |>
distinct(candidate_structure_inchikey_no_stereo)
)),
"annotations reranked at the",
cyan("(NPC) pathway"),
"level, \n",
magenta(nrow(
df_cla_sup |>
distinct(candidate_structure_inchikey_no_stereo)
)),
"annotations reranked at the",
magenta("(classyfire) superclass"),
"level, \n",
blue(nrow(
df_npc_sup |>
distinct(candidate_structure_inchikey_no_stereo)
)),
"annotations reranked at the",
blue("(NPC) superclass"),
"level, \n",
yellow(nrow(
df_cla_cla |>
distinct(candidate_structure_inchikey_no_stereo)
)),
"annotations reranked at the",
yellow("(classyfire) class"),
"level, \n",
green(nrow(
df_npc_cla |>
distinct(candidate_structure_inchikey_no_stereo)
)),
"annotations reranked at the",
green("(NPC) class"),
"level, and \n",
red(nrow(
df_cla_par |>
distinct(candidate_structure_inchikey_no_stereo)
)),
"annotations reranked at the",
red("(classyfire) parent"),
"level. \n",
"WITHOUT TAKING CONSISTENCY SCORE INTO ACCOUNT!"
)
)
rm(
df_cla_kin,
df_npc_pat,
df_cla_sup,
df_npc_sup,
df_cla_cla,
df_npc_cla,
df_cla_par
)
return(annot_table_wei_chemo)
}