From d840c1d1ec5df0dcabf94381245d29b6e265f064 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <kontrapunkt@uclmail.net>
Date: Thu, 12 Jan 2023 07:17:39 +0100
Subject: [PATCH] shiny-state, resources: Update defaults.
---
R/resources.R | 6 +++++-
R/shiny-state.R | 26 +++++++++++++-------------
2 files changed, 18 insertions(+), 14 deletions(-)
diff --git a/R/resources.R b/R/resources.R
index 7bda881..3bf1787 100644
--- a/R/resources.R
+++ b/R/resources.R
@@ -315,7 +315,7 @@ COLRDATA_KEY <- "set"
METFRAG_ADDUCTS = c("[M+H]+","[M+NH4]+","[M+Na]+","[M+K]+",
"[M+CH3OH+H]+","[M+ACN+H]+","[M+ACN+Na]+","[M+2ACN+H]+",
"[M-H]-","[M+Cl]-","[M+HCOO]-","[M+CH3COO]-","[M]+/-")
-METFRAG_WRITER_CHOICES = c("CSV","PSV","XLS")
+METFRAG_WRITER_CHOICES = c("CSV","PSV","XLS","ExtendedXLS","ExtendedFragmentXLS")
METFRAG_DEFAULT_WRITER = "CSV"
METFRAG_LOCAL_DATABASE_TYPE = c("LocalSDF","LocalPSV","LocalCSV")
METFRAG_REMOTE_DATABASE_TYPE = c("KEGG","PubChem","ExtendedPubChem")
@@ -334,3 +334,7 @@ METFRAG_STANDARD_SCORES = "FragmenterScore,OfflineIndividualMoNAScore" # Automat
# work
# well.
METFRAG_STANDARD_WEIGHTS = "1,1"
+METFRAG_DEFAULT_MAX_TREE_DEPTH = 2
+METFRAG_SAMPLE_NAME = "sample"
+METFRAG_DEFAULT_ABSMASSDEV = 1.E-3
+METFRAG_DEFAULT_RELMASSDEV = 5
diff --git a/R/shiny-state.R b/R/shiny-state.R
index c0401f1..a5d82d2 100644
--- a/R/shiny-state.R
+++ b/R/shiny-state.R
@@ -64,18 +64,18 @@ add_new_def_tag <- function(old_tags,how_many) {
#' @export
create_stub_gui <- function() {
- gui <- list()
+ gui = list()
shiny::isolate({
- gui$compounds <- shiny::reactiveValues(lists=character(),
+ gui$compounds = shiny::reactiveValues(lists=character(),
sets=character())
- gui$datatab <- shiny::reactiveValues(file=character(),
+ gui$datatab = shiny::reactiveValues(file=character(),
tag=character(),
adduct=character(),
set=character())
- gui$paths <- shiny::reactiveValues(project=NA_character_,
+ gui$paths = shiny::reactiveValues(project=NA_character_,
data=NA_character_)
- gui$project <- shiny::reactiveVal(NA_character_)
+ gui$project = shiny::reactiveVal(NA_character_)
})
gui
}
@@ -83,7 +83,7 @@ create_stub_gui <- function() {
create_gui <- function(project_path=NA_character_) {
shiny::isolate({
- gui <- create_stub_gui()
+ gui = create_stub_gui()
if (!is.na(project_path)) {
gui$paths$project = project_path
gui$project(basename(project_path))
@@ -555,12 +555,12 @@ make_metfrag_panel <- function(envopts) {
value=5),
numericInput("mf_fragment_peak_match_absolute_mass_deviation",
label="Fragment peak match absolute mass deviation",
- value=5),
+ value=METFRAG_DEFAULT_ABSMASSDEV),
numericInput("mf_fragment_peak_match_relative_mass_deviation",
label="Fragment peak match relative mass deviation",
- value=5),
+ value=METFRAG_DEFAULT_RELMASSDEV),
numericInput("mf_maximum_tree_depth", label="MaximumTreeDepth",
- value=2),
+ value=METFRAG_DEFAULT_MAX_TREE_DEPTH),
selectInput("mf_metfrag_candidate_writer",
label="MetFrag Candidate Writer",
choices=shinyscreen:::METFRAG_WRITER_CHOICES,
@@ -577,10 +577,10 @@ make_metfrag_panel <- function(envopts) {
choices=shinyscreen:::METFRAG_POSTPFLT_CHOICES,
selected=shinyscreen:::METFRAG_POSTPFLT_DEFAULT,
multiple=T),
- textInput("mf_score_types",label="Score
- Types",value=METFRAG_STANDARD_SCORES),
- textInput("mf_score_weights",label="Score Weights",
- value=METFRAG_STANDARD_WEIGHTS))
+ textInput("mf_score_types",label="Score Types",value=METFRAG_STANDARD_SCORES),
+ textInput("mf_score_weights",label="Score Weights",
+ value=METFRAG_STANDARD_WEIGHTS),
+ numericInput("mf_num_threads",label="Number of threads", value=1L))
}
--
GitLab