diff --git a/R/api.R b/R/api.R
index 2fd9615e1565294ca46104f62ae716b65f7073a7..ef73af147c04b68837eb03769fdae924c6dca779 100644
--- a/R/api.R
+++ b/R/api.R
@@ -403,13 +403,14 @@ conf_trans <- function(conf) {
##' @export
prescreen <- function(m) {
## Top-level auto prescreening function.
-
+ message("(prescreen): Start.")
confpres <- conf_trans_pres(m$conf$prescreen)
m$qa <- create_qa_table(m$extr,confpres)
m1 <- assess_ms1(m)
m <- assess_ms2(m1)
m$out$tab$summ <- gen_summ(m$out$tab$comp,m$qa$ms1,m$qa$ms2)
+ message("(prescreen): End.")
m
}
@@ -540,7 +541,7 @@ create_plots <- function(m) {
data.table::setkeyv(iflt_squish,plot_index)
ms1_plot <- m$extr$ms1[iflt_squish,
.(fig_eic={
- message("Progress: ",.GRP,"/",z.NGRP)
+ message("Progress: ",.GRP,"/",.NGRP)
df<-.SD
df$plot_label <- .SD[[..plot_ms1_label]]
res <- i.chunk[[1]][df,on=..plot_ms1_label]
diff --git a/R/resources.R b/R/resources.R
index 9b0a5e31ef7fd6e79f403a509e478485ffad28f2..b43233564d748a2824d8818d229dbb334be3e60a 100644
--- a/R/resources.R
+++ b/R/resources.R
@@ -241,3 +241,8 @@ EMPTY_SUMM <- data.table::data.table(set=character(0),
## Default sorting keys of spectra in the summary table
DEF_KEY_SUMM <- c(BASE_KEY_MS2,"an")
+
+
+SUBSET_VALS <- c(IGNORE="ignore",
+ GOOD="take the good ones",
+ BAD="take the bad ones")
diff --git a/inst/rmd/app.Rmd b/inst/rmd/app.Rmd
index 1f9e9f813dc84e5efa98da351f7c1b49e21a7547..a632fd4cd4f756799610518617759635a3631491 100644
--- a/inst/rmd/app.Rmd
+++ b/inst/rmd/app.Rmd
@@ -16,9 +16,7 @@ def_datatab <- shinyscreen:::dtable("tag"=factor(),
"set"=factor())
def_summ_subset <- shinyscreen:::dtable("QA Column"=shinyscreen:::QA_FLAGS,
- "Select"=factor("ignore",levels=c("ignore",
- "take the good ones",
- "take the bad ones")))
+ "Select"=factor("ignore",levels=shinyscreen:::SUBSET_VALS))
## RMassBank masks shiny::validate. Unmask it.
validate <- shiny::validate
## def_state$input$tab$tags <- def_datatab
@@ -289,12 +287,11 @@ Filter entries in the summary table according to the QA criteria.
* **qa_ms2_near** : MS2 spectrum is close enough to the MS1 peak
-For those who do not speak Italian (and do not dig the bad Sergio
-Leone pun):
+Values:
-* **l'irrelevante** : ignore QA criterion
-* **il buono** : entry passed QA
-* **il cattivo** : entry failed QA
+* **ignore** : ignore QA criterion
+* **take the good ones** : entry passed QA
+* **take the bad ones** : entry failed QA
</details>
```{r, echo=F}
@@ -473,10 +470,24 @@ the summary table_ configuration subsection.
</details>
</details>
+
+<div style="display: flex; vertical-align: top;">
+
+<div>
```{r, echo=FALSE}
actionButton(inputId = "presc_b",
- label = "Prescreen and filter")
+ label = "Prescreen")
+```
+</div>
+
+<div>
+```{r, echo=FALSE}
+actionButton(inputId = "sortsubset_b",
+ label = "Sort and subset")
```
+</div>
+
+</div>
```{r, echo=FALSE}
DT::dataTableOutput("summ_table")
@@ -624,6 +635,7 @@ update_gui <- function(in_conf, session) {
## Files
df <- shinyscreen:::file2tab(in_conf$data)
+ if ("File" %in% colnames(df)) {df$Files<-df$File;df$File<-NULL}
df[,tag:=as.character(tag),with=T]
rv_dfiles(df[,.(File=Files,tag),by=c("Files","tag"),mult="first"][,Files:=NULL])
print(rv_dfiles)
@@ -724,10 +736,11 @@ rf_conf_state <- reactive({
})
rf_get_subset <- reactive({
+ input$summ_subset
dt <- tryCatch(rhandsontable::hot_to_r(input$summ_subset),
error = function(e) def_summ_subset)
- dt[Select == "il buono", extra := T]
- dt[Select == "il cattivo", extra := F]
+ dt[Select == shinyscreen:::SUBSET_VALS[["GOOD"]], extra := T]
+ dt[Select == shinyscreen:::SUBSET_VALS[["BAD"]], extra := F]
sdt <- dt[!is.na(extra)]
if (NROW(sdt) > 0) {
sdt[,paste0(`QA Column`," == ",extra)]
@@ -766,6 +779,7 @@ observeEvent(input$project_b,{
wd <- tcltk::tk_choose.dir(default = getwd(),
caption = "Choose project directory")
message("Set project dir to ", wd)
+ dir.create(wd,recursive = T,showWarnings = F)
rv_state$conf$project <- wd
})
@@ -830,6 +844,11 @@ observe({
rv_datatab(res)
})
+observe({
+ mc <- rf_conf_state()
+ rv_state$conf <- mc$conf
+}, label = "conf_state")
+
observe({
dtab <- rv_datatab()
dfiles <- rv_dfiles()
@@ -837,6 +856,7 @@ observe({
print(dfiles)
message("(config) Generating mzml from rv.")
isolate(rv_state$input$tab$mzml <- dtab[dfiles,on="tag"])
+ message("(config) Done generating mzml from rv.")
}, label = "mzml_from_rv")
@@ -849,6 +869,7 @@ observe({
res <- dtab[dfiles,on="tag"]
data.table::setnames(res,"File","Files")
isolate(rv_state$input$tab$mzml <- res)
+ message("(config) Generating mzml from inputs.")
}, label = "mzml_from_inp")
@@ -859,21 +880,17 @@ observeEvent(input$extract_b,{
paste0("extract.",shinyscreen:::FN_CONF))
yaml::write_yaml(x=m$conf,file=fn_c_state)
message("(extract) Config written to ", fn_c_state)
- state <- withr::with_dir(new=m$conf$project,
- code = {
- m <- setup_phase(m)
- m <- mk_comp_tab(m)
- extr_data(m)
- })
+ state <- shinyscreen::run(m=m,
+ phases=c("setup",
+ "comptab",
+ "extract"))
message("(extract) Done extracting.")
z <- shinyscreen::merge2rev(rv_state,lst = state)
- eval(z)
- ## rv_state <<- list2rev(state)
-
+ eval(z)
})
observeEvent(input$presc_b,{
- validate(need(NROW(rv_state$extr$ms) > 0,
+ validate(need(NROW(rv_state$extr$ms1) > 0,
message = "Perform extraction first."))
m <- rev2list(rv_state)
@@ -881,18 +898,32 @@ observeEvent(input$presc_b,{
paste0("presc.",shinyscreen:::FN_CONF))
yaml::write_yaml(x=m$conf,file=fn_c_state)
message("(prescreen) Config written to ", fn_c_state)
- state <- withr::with_dir(new=m$conf$project,
- code = {
- m <- prescreen(m)
- m <- sort_spectra(m)
- subset_summary(m)
- })
+ state <- shinyscreen::run(m=m,
+ phases=c("prescreen"))
message("(prescreen) Done prescreening.")
z <- shinyscreen::merge2rev(rv_state,lst = state)
eval(z)
+})
+
+observeEvent(input$sortsubset_b,{
+ m <- rev2list(rv_state)
+
+ fn_c_state <- file.path(m$conf$project,
+ paste0("sortsubset.",shinyscreen:::FN_CONF))
+ yaml::write_yaml(x=m$conf,file=fn_c_state)
+ message("(sortsubset) Config written to ", fn_c_state)
+ state <- shinyscreen::run(m=m,
+ phases=c("sort",
+ "subset"))
+ message("(sortsubset) Done with sorting and subsetting.")
+
+ z <- shinyscreen::merge2rev(rv_state,lst = state)
+ eval(z)
+
+
})
observeEvent(input$plot_b,{
@@ -904,11 +935,9 @@ observeEvent(input$plot_b,{
paste0("genplot.",shinyscreen:::FN_CONF))
yaml::write_yaml(x=m$conf,file=fn_c_state)
message("(generate plots) Config written to ", fn_c_state)
- state <- withr::with_dir(new=m$conf$project,
- code = {
- m <- create_plots(m)
- save_plots(m)
- })
+ state <- shinyscreen::run(m=m,
+ phases=c("plot",
+ "saveplot"))
message("(generate plots) Done generating plots.")
z <- shinyscreen::merge2rev(rv_state,lst = state)