diff --git a/R/api.R b/R/api.R
index 49065f5277171daca4ba244ce56f64045b6a8a7c..feb653eafef7a36ac14a0ab57a6c9855fac6a4c0 100644
--- a/R/api.R
+++ b/R/api.R
@@ -143,7 +143,7 @@ mk_comp_tab <- function(m) {
comp <- cmpds[setid,on="ID"][mzml,.(tag,adduct,ID,RT,set,Name,Files,wd,SMILES,Formula,mz,known),on="set",allow.cartesian=T]
tab2file(tab=comp,file=paste0("setidmerge",".csv"))
setkey(comp,known,set,ID)
-
+
## Known structure.
## comp[,`:=`(mz=mapply(calc_mz_from_smiles,SMILES,adduct,ID,USE.NAMES = F))]
comp[known=="structure",`:=`(mz=calc_mz_from_smiles(SMILES,adduct,ID))]
@@ -275,6 +275,7 @@ extr_data <- function(m) {
## Reduce the comp table to only unique masses (this is because
## different sets can have same masses).
+
m$out$tab$data <- m$out$tab$comp[,head(.SD,1),by=c('adduct','tag','ID')]
m$out$tab$data[,set:=NULL] #This column is meaningless now.
files <- m$out$tab$data[,unique(Files)]
@@ -352,6 +353,9 @@ extr_data <- function(m) {
message('Done saving extracted data.')
m$extr$tmp <- NULL
+ timetag <- format(Sys.time(), "%Y%m%d_%H%M%S")
+ saveRDS(object = m, file = file.path(m$conf$project,
+ paste0(timetag,"_",FN_EXTR_STATE)))
m
}
diff --git a/R/mix.R b/R/mix.R
index 3a987b6d6f0c5c4082ed2518c3005f9854872475..f0268b7f4cf94b66ef0bc5fa8d992d30299410cc 100644
--- a/R/mix.R
+++ b/R/mix.R
@@ -89,7 +89,7 @@ calc_mz_from_formula <- function(chform,adduct,id) {
charge=Charge),on=""])
names(uadds) <- uad
adds <- rbindlist(l=lapply(adduct,function(a) uadds[[a]]))
-
+
merger <- function (mol_form,add,ded) {
res <- numeric(length(mol_form))
both_ind <- which(add != 'FALSE' & ded != 'FALSE')
@@ -106,6 +106,19 @@ calc_mz_from_formula <- function(chform,adduct,id) {
res
}
forms <- merger(mol_form,adds$add,adds$ded)
+
+ ## Check if formulas actually calculated.
+ bad_idx <- which(forms=="0")
+ bad_adducts <- adduct[bad_idx]
+ bad_ids <- id[bad_idx]
+ non_dups <- !duplicated(bad_idx)
+ bad_ids <- bad_ids[non_dups]
+ bad_adducts <- bad_adducts[non_dups]
+ if (length(bad_idx)>0) stop(paste0("Unable to process the adducts:\n",
+ paste(bad_adducts,collapse = ","),
+ "\nfor id-s:",
+ paste(bad_ids,collapse = ",")))
+
mz <- the_ifelse(!is.na(forms),
mapply(function(ff,ch) enviPat::isopattern(ISOTOPES,chemforms = ff,
charge = ch, verbose = F)[[1]][1],
diff --git a/R/resources.R b/R/resources.R
index 6ff657b6915af578a917e9e5ba0e6611a6c9a6c6..cf29d7080d5e7872f683a7822ef58e1e223e20ba 100644
--- a/R/resources.R
+++ b/R/resources.R
@@ -33,6 +33,7 @@ FN_LOC_SETID <-"setid.csv"
FN_COMP_TAB<-"comprehensive.csv"
FN_SPEC<-"specdata.rds"
FN_CONF <- "conf-state.yaml"
+FN_EXTR_STATE <- "state_after_extraction.rds"
.envp <- new.env(parent = emptyenv())
data(adducts,package = "enviPat", envir = .envp)
data(isotopes,package = "enviPat", envir = .envp)
diff --git a/inst/rmd/app.Rmd b/inst/rmd/app.Rmd
index 619eeb522593b2c5adcf1d27c83d8e40afea6952..3641fc0686f1b1af74522028cd538424cf371a41 100644
--- a/inst/rmd/app.Rmd
+++ b/inst/rmd/app.Rmd
@@ -300,12 +300,6 @@ Leone pun):
rhandsontable::rHandsontableOutput("summ_subset")
-## checkboxGroupInput("summ_subset",
-## label=NULL,
-## choiceNames = shinyscreen:::QA_FLAGS,
-## choiceValues = shinyscreen:::QA_FLAGS)
-
-
```
</div>
@@ -328,23 +322,6 @@ rhandsontable::rHandsontableOutput("order_summ")
</div>
-
-
-
-<!-- <details><summary>Order entries</summary> -->
-
-<!-- Sequence of column a -->
-
-<!-- </details> -->
-<!-- ```{r, echo=F} -->
-<!-- checkboxGroupInput("summ_subset", -->
-<!-- label=NULL, -->
-<!-- choiceNames = shinyscreen:::QA_FLAGS, -->
-<!-- choiceValues = 1:length(shinyscreen:::QA_FLAGS)) -->
-
-<!-- ``` -->
-
-
## Plots
### Logarithmic axis
@@ -488,17 +465,16 @@ rf_conf_proj <- reactive({
rf_conf_state <- reactive({
state <- rf_conf_proj()
- mzml1 <- rf_get_inp_datatab()
- mzml1[,`:=`(tag=as.character(tag),
- set=as.character(set),
- adduct=as.character(adduct))]
- mzml2 <- rf_get_inp_datafiles()
+ ## mzml1 <- rf_get_inp_datatab()
+ ## mzml1[,`:=`(tag=as.character(tag),
+ ## set=as.character(set),
+ ## adduct=as.character(adduct))]
+ ## mzml2 <- rf_get_inp_datafiles()
+
+ ## mzml <- mzml1[mzml2,on="tag"]
- mzml <- mzml1[mzml2,on="tag"]
- data.table::setnames(mzml,"File","Files")
ftab <- get_fn_ftab(state)
state$conf$data <- ftab
- state$input$tab$mzml <- mzml
state$conf[["summary table"]]$filter <- rf_get_subset()
state$conf[["summary table"]]$order <- rf_get_order()
state
@@ -517,8 +493,8 @@ rf_get_subset <- reactive({
rf_get_order <- reactive({
dt <- tryCatch(rhandsontable::hot_to_r(input$order_summ),error = function(e) def_ord_summ)
- dt[Direction == "descending",`Column Name` := paste0("-",`Column Name`)]
- dt[,`Column Name`]
+ tmp <- dt[Direction == "descending",.(`Column Name`=paste0("-",`Column Name`))]
+ tmp[,`Column Name`]
})
rf_get_inp_datatab <- eventReactive(input$datatab,{
@@ -582,11 +558,9 @@ observeEvent(input$datafiles_b,{
observe({
df_tab <- rf_get_inp_datafiles()
state <- rf_compound_input_state()
-
isolate(oldtab <- rf_get_inp_datatab())
-
+
oldt <- oldtab$tag
-
tagl <- df_tab$tag
diff <- setdiff(tagl,
oldt)
@@ -613,20 +587,39 @@ observe({
rv_datatab(res)
})
+observe({
+ dtab <- rv_datatab()
+ dfiles <- rv_dfiles()
+ message("(config) Generating mzml from rv.")
+ isolate(rv_state$input$tab$mzml <- dtab[dfiles,on="tag"])
+
+}, label = "mzml_from_rv")
+
+observe({
+ dtab <- rf_get_inp_datatab()
+ dfiles <- rf_get_inp_datafiles()
+
+ message("(config) Generating mzml from inputs.")
+ res <- dtab[dfiles,on="tag"]
+ data.table::setnames(res,"File","Files")
+ isolate(rv_state$input$tab$mzml <- res)
+
+
+}, label = "mzml_from_inp")
observeEvent(input$extract_b,{
- tmp <- rf_conf_state()
- fn_c_state <- file.path(tmp$conf$project,
+ m <- rf_conf_state()
+ fn_c_state <- file.path(m$conf$project,
paste0("extract.",shinyscreen:::FN_CONF))
- yaml::write_yaml(x=tmp$conf,file=fn_c_state)
+ yaml::write_yaml(x=m$conf,file=fn_c_state)
message("(extract) Config written to ", fn_c_state)
- state <- withr::with_dir(new=tmp$conf$project,
+ state <- withr::with_dir(new=m$conf$project,
code = {
- m <- setup_phase(tmp)
- m <- mk_comp_tab(tmp)
- extr_data(tmp)
+ m <- setup_phase(m)
+ m <- mk_comp_tab(m)
+ extr_data(m)
})
message("(extract) Done extracting.")
rv_state <- list2rev(state)
@@ -732,7 +725,7 @@ observeEvent(input$conf_file_load_b,
## Files
df <- shinyscreen:::file2tab(conf$data)
-
+ df[,tag:=as.character(tag),with=T]
rv_dfiles(df[,.(File=Files,tag)])
nms <- colnames(df)
nms <- nms[nms!="Files"]