From 9413f2212ff90bec626f66c077c01d958689820a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <todor.kondic@uni.lu>
Date: Thu, 1 Oct 2020 11:18:03 +0200
Subject: [PATCH] api: Add sort_spectra
* R/api.R(sort_spectra): New function to sort the spectral table.
* R/resources.R(DEF_ORDER_SPECTRA): New parameter defining the default
order of the spectral table.
* NAMESPACE: Update exports.
---
NAMESPACE | 3 +++
R/api.R | 15 +++++++++++++--
R/resources.R | 2 ++
3 files changed, 18 insertions(+), 2 deletions(-)
diff --git a/NAMESPACE b/NAMESPACE
index 88439a8..fe5d4c0 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,5 +1,6 @@
# Generated by roxygen2: do not edit by hand
+export(concurrency)
export(conf_trans)
export(extr_data)
export(extract)
@@ -9,8 +10,10 @@ export(load_compound_input)
export(load_data_input)
export(load_inputs)
export(mk_comp_tab)
+export(mk_tol_funcs)
export(prescreen)
export(run)
export(run_in_dir)
+export(sort_spectra)
import(data.table)
importFrom(shiny,validate)
diff --git a/R/api.R b/R/api.R
index 3cb675b..e011f54 100644
--- a/R/api.R
+++ b/R/api.R
@@ -172,7 +172,7 @@ verify_data <- function(conf,all_sets) {
return(conf)
}
-## @export
+#' @export
concurrency <- function(m) {
## Reads the concurrency entry in the config. It is optional, if
## not given, then it is up to the user to define the plan of the
@@ -204,6 +204,7 @@ concurrency <- function(m) {
m
}
+#' @export
mk_tol_funcs <- function(m) {
## Depending on units given when the user specified the errors,
## generate functions that calculate errors given the concrete
@@ -277,7 +278,7 @@ extr_data <- function(m) {
msk <- sapply(tmp,future::resolved)
curr_done <- which(msk)
- names(msk) <- files
+ names(msk) <- ftags$Files
for (x in curr_done) {
message("Done extraction for ", names(msk)[[x]])
@@ -324,3 +325,13 @@ prescreen <- function(m) {
m$out$tab$ftab <- merge(m$out$tab$comp,m$qa$ms[,..fields],by=c("Files","adduct","ID"))
m
}
+
+##' @export
+sort_spectra <- function(m) {
+ ## Sorts the spectral table (ftab) in order specified either in
+ ## `order spectra` sublist of m$conf, or if that is null, the
+ ## DEF_ORDER_SPECTRA.
+ order <- if (!is.null(m$conf[["order spectra"]])) m$conf[["order spectra"]] else DEF_ORDER_SPECTRA
+ data.table::setkeyv(m$out$tab$ftab,order)
+ m
+}
diff --git a/R/resources.R b/R/resources.R
index d62a74f..60c37f5 100644
--- a/R/resources.R
+++ b/R/resources.R
@@ -183,3 +183,5 @@ QA_NUM_INT <- c("sel_ms2","ind_ms1_rt")
QA_COLS <- c(QA_FLAGS,QA_NUM_REAL,QA_NUM_INT)
+## Default order of spectra in spectral table
+DEF_ORDER_SPECTRA <- c("set","qa_pass","int_ms1","adduct","mz","tag")
--
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