From b49b58459bcb551842be1857ce5c543cfaa29d14 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <todor.kondic@uni.lu>
Date: Fri, 1 Jul 2022 10:40:21 +0200
Subject: [PATCH] app: shiny-state: app state to program state conversion.
---
R/shiny-state.R | 55 +++++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 55 insertions(+)
diff --git a/R/shiny-state.R b/R/shiny-state.R
index f9f246e..fb632a7 100644
--- a/R/shiny-state.R
+++ b/R/shiny-state.R
@@ -74,6 +74,12 @@ r2datatab <- function(rdatatab) {
data.table(tag=tag,adduct=adduct,set=set,file=file)
}
+r2taadse <- function(tablist,sets) {
+ data.table(tag=factor(tablist$tag,levels=unique(tablist$tag)),
+ adduct=factor(tablist$adduct,levels=ADDUCTMAP),
+ set=factor(tablist$set,levels=sets))
+}
+
r2compounds <- function(rcompounds) {
shiny::isolate({
cmpd_lists <- rcompounds$lists
@@ -162,3 +168,52 @@ unpack_app_state <- function(session,input,project_path,packed_state) {
}
+
+
+input2conf <- function(input,conf=list()) {
+ conf$compounds <- list()
+ conf$figures <- list()
+ conf$prescreen <- list()
+ conf$tolerance <- list()
+ conf$extract <- list()
+ conf$summary_table <- list()
+ conf$report <- list()
+
+ conf$debug <- "no"
+
+ conf$compounds$lists <- gui$compounds$lists
+ conf$compounds$sets <- gui$compounds$sets
+
+ conf$tolerance[["ms1 fine"]] <- paste(input$ms1_fine,input$ms1_fine_unit)
+ conf$tolerance[["ms1 coarse"]] <- paste(input$ms1_coarse,input$ms1_coarse_unit)
+ conf$tolerance[["eic"]] <- paste(input$ms1_eic,input$ms1_eic_unit)
+ conf$tolerance[["rt"]] <- paste(input$ret_time_shift_tol,input$ret_time_shift_tol_unit)
+
+ conf$prescreen[["ms1_int_thresh"]] <- input$ms1_int_thresh
+ conf$prescreen[["ms2_int_thresh"]] <- input$ms2_int_thresh
+ conf$prescreen[["s2n"]] <- input$s2n
+ conf$prescreen[["ret_time_shift_tol"]] <- paste(input$ret_time_shift_tol,input$ret_time_shift_tol_unit)
+
+ conf$figures$rt_min <- paste(input$plot_rt_min,input$plot_rt_min_unit)
+ conf$figures$rt_max <- paste(input$plot_rt_max,input$plot_rt_max_unit)
+ conf$figures$ext <- input$plot_ext
+
+ conf$extract$missing_precursor_info <- input$missingprec
+
+ conf$report$author <- input$rep_aut
+ conf$report$title <- input$rep_aut
+
+ conf
+}
+
+app_state2state <- function(input,gui) {
+ shiny::req(gui$paths$project)
+ m <- new_project(gui$paths$project)
+ m$run$paths <- shiny::reactiveValuesToList(gui$paths)
+ m$conf <- input2conf(input)
+ m
+}
+
+
+
+
--
GitLab