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Commit 654106c4 authored by Todor Kondic's avatar Todor Kondic
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R/shiny-state.R
+ 6
− 0
View file @ 654106c4
......@@ -28,6 +28,8 @@ GUI_ALL_INPUTS <- c(GUI_SELECT_INPUTS,
GUI_TEXT_INPUTS,
GUI_RADIO_INPUTS)
#' @export
create_stub_gui <- function() {
gui <- list()
......@@ -298,3 +300,7 @@ pre_extr_val_block <- function(m) {
return(T)
}
commit_val_block <- function(gui) {
}
R/shiny-ui-base.R
+ 73
− 27
View file @ 654106c4
......@@ -430,7 +430,18 @@ mk_shinyscreen_server <- function(projects,init) {
## The reactive world.
rvs <- reactiveValues(m=def_state,
gui=create_gui())
gui=create_gui(),
status=reactiveValues(is_extracted_stat=NA_character_,
is_qa_stat=NA_character_,
ms1_coarse_stat=NA_character_,
ms1_fine_stat=NA_character_,
ms1_eic_stat=NA_character_,
rt_stat=NA_character_,
ms1_int_thresh_stat=NA_character_,
ms2_int_thresh_stat=NA_character_,
s2n_stat=NA_character_,
ret_time_shift_tol_stat=NA_character_))
compl_sets <- eventReactive(rvs$m$input$tab$setid,
rvs$m$input$tab$setid[,unique(set)])
......@@ -744,60 +755,89 @@ mk_shinyscreen_server <- function(projects,init) {
message("project: ",rvs$gui$project())
}, label = "project-b")
observe({
rvs$gui$paths$project
rvs$gui$paths$data
rvs$gui$datatab$file
rvs$gui$datatab$tag
rvs$gui$datatab$set
rvs$gui$datatab$adduct
rvs$gui$compounds$lists
rvs$gui$compounds$sets
input$missingprec
## observe({
## rvs$gui$paths$project
## rvs$gui$paths$data
## rvs$gui$datatab$file
## rvs$gui$datatab$tag
## rvs$gui$datatab$set
## rvs$gui$datatab$adduct
## rvs$gui$compounds$lists
## rvs$gui$compounds$sets
## input$missingprec
input$ms1_fine
input$ms1_fine_unit
## input$ms1_fine
## input$ms1_fine_unit
input$ms1_coarse
input$ms1_coarse_unit
## input$ms1_coarse
## input$ms1_coarse_unit
input$ms1_eic
input$ms1_eic_unit
## input$ms1_eic
## input$ms1_eic_unit
input$ms1_rt_win
input$ms1_rt_win_unit
## input$ms1_rt_win
## input$ms1_rt_win_unit
input$missingprec
## input$missingprec
isolate({
rvs$m$conf <- input2conf_setup(gui=rvs$gui,conf=rvs$m$conf,input=input)
})
## isolate({
## rvs$m$conf <- input2conf_setup(gui=rvs$gui,conf=rvs$m$conf,input=input)
## })
message("Initial parameters updated.")
}, label = "gen-setup-state")
## message("Initial parameters updated.")
## }, label = "gen-setup-state")
observeEvent(input$commit_changes,{
rvs$m$conf <- input2conf_setup(input=input,gui=rvs$gui,conf=rvs$conf)
rvs$m$conf <- input2conf_prescreen(input=input,conf=rvs$conf)
},label="comm-changes")
observeEvent(input$extract_b,{
req(isTruthy(pre_extr_val_block(rvs$m)))
rvs$status$ms1_coarse = rvs$m$conf$tolerance[["ms1 coarse"]]
rvs$status$ms1_fine = rvs$m$conf$tolerance[["ms1 fine"]]
rvs$status$ms1_eic_stat = rvs$m$conf$tolerance[["eic"]]
rvs$status$rt_stat = rvs$m$conf$tolerance[["rt"]]
rvs$status$is_extracted_stat = "In process."
})
observeEvent(input$extract_b,{
req(isTruthy(pre_extr_val_block(rvs$m)))
shinymsg("Extraction has started. This may take a while.")
rvs$m <- run(m=rvs$m,phases="extract")
rvs$m <- run(m=rvs$m,phases=c("setup","extract"))
message("(extract) Done extracting.")
fn_c_state <- file.path(rvs$m$run$paths$project,
paste0("extract.",shinyscreen:::FN_CONF))
yaml::write_yaml(x=rvs$m$conf,file=fn_c_state)
message("(extract) Config written to ", fn_c_state)
shinymsg("Extraction has been completed.")
rvs$status$is_extracted_stat = "Yes."
})
observeEvent(input$presc_b,{
rvs$status$ms1_int_thresh_stat = rvs$m$conf$prescreen[["ms1_int_thresh_stat"]]
rvs$status$ms2_int_thresh_stat = rvs$m$conf$prescreen[["ms2_int_thresh_stat"]]
rvs$status$s2n_stat = rvs$m$conf$prescreen[["s2n"]]
rs$status$ret_time_shift_tol_stat = rvs$m$conf$prescreen[["ret_time_shift_tol"]]
rvs$status$is_qa_stat = "No."
})
observeEvent(input$presc_b,{
shinymsg("Prescreening started. Please wait.")
rvs$m <- rf_prescreen_state()
rvs$m <- run(m=rvs$m,phases="prescreen")
message("(prescreen) Done prescreening.")
shinymsg("Prescreening completed.")
## TODO TODO TODO see also rvs statuses.
})
......@@ -988,6 +1028,12 @@ mk_shinyscreen_server <- function(projects,init) {
deferRender = T,
scroller = T))
})
output$is_extracted_txt <- renderText({
"No."
})
output$is_qa_txt <- renderText({"No."})
}
......
inst/rmd/app.Rmd
+ 21
− 1
View file @ 654106c4
......@@ -585,7 +585,7 @@ DT::DTOutput("summ_subset")
<div style="padding-left: 3em">
#### Control
<div style="display: flex;flex-flow: row nowrap;">
<div style="display: flex;flex-flow: row wrap;">
```{r, echo=F}
actionButton(inputId= "commit_changes",
label = "Commit configuration")
......@@ -600,6 +600,26 @@ actionButton(inputId = "presc_b",
label = "Prescreen")
```
</div>
#### Status
- Has the data been extracted? `r htmlOutput("is_extracted_stat", inline=T)`
- Has the data been auto-quality checked? `r htmlOutput("is_qa_stat", inline=T)`
##### Extraction
- MS1 coarse: `r htmlOutput("ms1_coarse_stat", inline=T)`
- MS1 fine: `r htmlOutput("ms1_fine_stat", inline=T)`
- MS1 eic: `r htmlOutput("ms1_eic_stat", inline=T)`
- Retention time window: `r htmlOutput("rt_stat", inline=T)`
##### Prescreening
- Intensity Threshold (MS1): `r htmlOutput("ms1_int_thresh_stat", inline=T)`
- Intensity Threshold (MS2): `r htmlOutput("ms2_int_thresh_stat", inline=T)`
- Retention time shift: `r htmlOutput("s2n_stat", inline=T)`
- Signal-to-noise ratio: `r htmlOutput("ret_time_shift_tol_unit_stat", inline=T)`
</div>
</div>
......
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