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resources.R 7.81 KiB
## Copyright (C) 2020,2021 by University of Luxembourg
## Licensed under the Apache License, Version 2.0 (the "License");
## you may not use this file except in compliance with the License.
## You may obtain a copy of the License at
## http://www.apache.org/licenses/LICENSE-2.0
## Unless required by applicable law or agreed to in writing, software
## distributed under the License is distributed on an "AS IS" BASIS,
## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
## See the License for the specific language governing permissions and
## limitations under the License.
## Config defaults
CONF <- list(data=NA_character_,
project=getwd(),
compounds=list(lists=list(),
sets=NA_character_))
## Constants
FN_SUMM_BASE<-"summ.base.csv"
FN_SUMM_PP<-"summ.pp.csv"
FN_PP_OUT_PREF<-"PP.filetable"
FN_SUMM_STATE<-"summ_state.csv"
FN_SUMM <- "summ.csv"
FN_SUMM_DEF_OUT <- FN_SUMM
FN_CMP_L<-"compounds.csv"
FN_LOC_SETID <-"setid.csv"
FN_COMP_TAB<-"comprehensive.csv"
FN_SPEC<-"specdata.rds"
FN_CONF <- "conf-state.yaml"
FN_EXTR_STATE <- "state_after_extraction.rds"
.envp <- new.env(parent = emptyenv())
data(adducts,package = "enviPat", envir = .envp)
data(isotopes,package = "enviPat", envir = .envp)
ADDUCTS <- dtable(.envp$adducts)
ISOTOPES <- dtable(.envp$isotopes)
.envp <- NULL
ADDUCTMAP <- ADDUCTS$Name
ADDUCTS$Name <- the_ifelse(ADDUCTS$Charge>0,paste0("[",ADDUCTS$Name,"]+"),paste0("[",ADDUCTS$Name,"]-"))
## names(ADDUCTMAP) <- apply(ADDUCTS,1,function(row) {
## nm <- row[["Name"]]
## sgn <- row[["Charge"]]
## suff <- if (sgn > 0) "+" else if (sgn < 0) "-" else ""
## paste0("[",nm,"]",suff)
## })
## ADDUCTS$Name <- names(ADDUCTMAP)
DISP_ADDUCTS <- ADDUCTS$Name
TAG_NA <- "::UNSET::"
SET_NA <- "::UNSET::"
TAG_DEF <- TAG_NA
TAG_DEF_DESC<-"Case"
DEFAULT_RT_RANGE=c(NA,NA)
DEFAULT_INT_RANGE=c(NA,NA)
DEFAULT_MZ_RANGE=c(NA,NA)
## QANAMES <- c("MS1","MS2","Alignment","AboveNoise")
PLOT_DEF_TAGS<-NA
PLOT_DEF_SET<-NA
CEX<-0.75
RT_DIGITS=2
M_DIGITS=4
PAL="Dark2"
REST_TAB<-c("mzml")
GUI_TAB_TITLE<-c(conf="Config",
gen="Spectra Extraction and Automatic QA",
pres="Prescreening",
log="Log")
GUI_SIDE_TITLE<-GUI_TAB_TITLE
GUI_SIDE_TITLE[["gen"]]<-"Spectra Extraction"
CHR_GRAM_X="retention time [min]"
CHR_GRAM_Y="intensity"
KEY_GLYPH='rect'
PLOT_MS1_LEG_TIT<-"peak retention time (MS1)"
PLOT_MS2_LEG_TIT<-"peak retention time (MS2)"
MS2_1ST_N<-5
EXTR_MS2_DIR<-"MS2"
EXTR_MS2_FLAG<-file.path(EXTR_MS2_DIR,'.ms2.DONE')
SUMM_CHK_NONE<-'NONE'
SUMM_CHK_AUTO<-'AUTO'
SUMM_CHK_MANL<-'MANUAL'
MS1_ERR_COARSE<-0.5 # Da
MS1_ERR_FINE<- 5 # ppm
EIC_ERR <- 0.001 # Da
RT_EXTR_ERR<-0.5 # min
RT_SHIFT_ERR <- 0.5 # min
MS1_INT_THOLD <- 1e5
MS2_INT_THOLD <- 5000.
MS1_SN_FAC <- 3.0
## Shiny objects
NUM_INP_WIDTH=40
NUM_INP_HEIGHT="5%"
## Possible compound list fields
EMPTY_CMPD_LIST <- dtable(ID=character(),
SMILES=character(),
Name=character(),
Formula=character(),
RT=numeric(),
mz=numeric(),
known=character(),
ORIG=character())
COMP_LIST_COLS <- c("ID","Name","SMILES","Formula","RT","mz")
## Comprehensive table properties
COMP_NAME_MAP <- list(RT="rt")
COMP_NAME_FIRST <- c("ID","mz","rt","adduct","tag","set","Name","known","SMILES","Formula","file")
## Trivial data tableEMPTY_MZML <- dtable(file=character(0),
tag=character(0),
adduct=character(0),
set=character(0))
FN_DATA_TAB <- "data-files.csv"
## Default number of concurrent workers
NO_WORKERS <- 2
## Input parameters for prescreening.
CONF_PRES_NUM <- c("ms1_int_thresh","ms2_int_thresh","s2n")
CONF_PRES_TU <- c("ret_time_shift_tol")
## Prescreening columns
QA_FLAGS <- c("qa_pass",
"qa_ms1_exists",
"qa_ms2_exists",
"qa_ms1_good_int",
"qa_ms1_above_noise",
"qa_ms2_near",
"qa_ms2_good_int")
QA_NUM_REAL <- c("ms1_int","ms1_rt","ms1_mean")
QA_NUM_INT <- c("ms2_sel","ms1_rt_ind")
QA_COLS <- c(QA_FLAGS,QA_NUM_REAL,QA_NUM_INT)
## MS2 spectral table columns
MS2_SPEC_COLS <- c("adduct","tag","ID","CE","rt","file","spec","ms2_max_int")
## MS1 spectral table columns
MS1_SPEC_COLS <- c("adduct","tag","ID","eicMS1","ms1_int","ms1_rt","ms1_mean")
## Default secondary indexing in the summary table
DEF_INDEX_SUMM <- c("set", "-qa_pass", "-ms1_int", "adduct","-mz")
## Top-level directory to store the figures
FIG_TOPDIR <- "figures"
## Figure filter
FIG_DEF_FILTER <- ""
FIG_DEF_SUBSET <- c("set","adduct","ID")
REPORT_AUTHOR <- "Anonymous"
REPORT_TITLE <- "Plots of EICs and MS2 Spectra"
## Select the most fundamental group of entries. Within this group,
## each ID is unique.
BASE_KEY <- c("adduct","tag","ID")
BASE_KEY_MS2 <- c(BASE_KEY,"CE")
FIG_DEF_CONF <-list(grouping=list(group="adduct",
plot="ID",
label="tag"))
## File table properties
SUMM_COLS=c("set",BASE_KEY_MS2,"an","mz","ms1_rt", "ms1_int", "ms2_rt", "ms2_int",
"ms1_mean","ms2_sel",QA_FLAGS,"Name", "SMILES", "Formula", "known","Comments","file")
PLOT_FEATURES <- c("adduct",
"tag", "ID")
## Empty summary table.
EMPTY_SUMM <- data.table::data.table(set=character(0),
adduct=character(0),
tag=character(0),
ID=character(0),
CE=character(0),
an=integer(0),
mz=numeric(0),
ms1_rt=numeric(0),
ms1_int=numeric(0),
ms2_rt=numeric(0),
ms2_int=numeric(0),
ms1_mean=numeric(0),
ms2_sel=logical(0),
qa_pass=logical(0),
qa_ms1_exists=logical(0),
qa_ms2_exists=logical(0),
qa_ms1_good_int=logical(0),
qa_ms1_above_noise=logical(0),
qa_ms2_near=logical(0),
qa_ms2_good_int=logical(0),
Name=character(0),
SMILES=character(0),
Formula=character(0),
known=character(0),
Comments=character(0),
file=character(0))
## Default sorting keys of spectra in the summary table
DEF_KEY_SUMM <- c(BASE_KEY_MS2,"an")
SUBSET_VALS <- c(IGNORE="ignore",
GOOD="select good",
BAD="select bad")
## Empty comprehensive table.
EMPTY_COMP_TAB <- dtable(ID=character(),
mz=numeric(),
rt=numeric(),
adduct=character(),
tag=character(),
set=character(),
Name=character(),
known=character(),
SMILES=character(),
Formula=character(),
file=character())
DEF_CONF_MISSING_PCS <- "do_nothing"
## Significant digits for output
SIGNF_I <- 3
SIGNF_MZ <- 7
SIGNF_RT <- 4
## Symbols to display T, or F
SYM_YES="\U002713"
SYM_NO="\U00274C"