diff --git a/R/api.R b/R/api.R
index 55f996a9503138cc729d80735f1e73f59dd140bb..49065f5277171daca4ba244ce56f64045b6a8a7c 100644
--- a/R/api.R
+++ b/R/api.R
@@ -75,7 +75,7 @@ load_compound_input <- function(m) {
fns <- m$conf$compounds$lists
for (l in 1:length(fns)) {
fn <- fns[[l]]
- fnfields <- colnames(fn)
+ # fnfields <- somehow read the file columns in
dt <- file2tab(fn, colClasses=c(ID="character",
SMILES="character",
Formula="character",
@@ -83,8 +83,8 @@ load_compound_input <- function(m) {
RT="numeric",
mz="numeric"))
verify_cmpd_l(dt=dt,fn=fn)
- nonexist <- setdiff(fnfields,fields)
- coll[[l]] <- if (length(nonexist)==0) dt else dt[,(nonexist) := NULL]
+ # nonexist <- setdiff(fnfields,fields)
+ coll[[l]] <- dt #if (length(nonexist)==0) dt else dt[,(nonexist) := NULL]
coll[[l]]$ORIG <- fn
}
@@ -102,6 +102,9 @@ load_compound_input <- function(m) {
msg <- paste(paste('Duplicate IDs', fndupID,'found in',fn),msg,sep = '\n')
}
+ ## TODO: Should we just kick out the duplicates, instead of
+ ## erroring?
+
assert(all(!dups), msg = msg)
cmpds[,("known"):=.(the_ifelse(!is.na(SMILES),"structure",the_ifelse(!is.na(Formula),"formula","mz")))]
diff --git a/R/resources.R b/R/resources.R
index 34890a378780e7904b6cbe59f37861f94adf4097..6ff657b6915af578a917e9e5ba0e6611a6c9a6c6 100644
--- a/R/resources.R
+++ b/R/resources.R
@@ -48,7 +48,7 @@ ADDUCTS$Name <- the_ifelse(ADDUCTS$Charge>0,paste0("[",ADDUCTS$Name,"]+"),paste0
## paste0("[",nm,"]",suff)
## })
## ADDUCTS$Name <- names(ADDUCTMAP)
-DISP_ADDUCTS <- c("UNSET",ADDUCTS$Name)
+DISP_ADDUCTS <- ADDUCTS$Name
TAG_NA <- "::UNSET::"
SET_NA <- "::UNSET::"
TAG_DEF <- TAG_NA
diff --git a/inst/rmd/app.Rmd b/inst/rmd/app.Rmd
index 061496f39a31f8bf03c24ef10782e26ecde4dfdc..5b7854f0cefecc283804dadc951f752382528de8 100644
--- a/inst/rmd/app.Rmd
+++ b/inst/rmd/app.Rmd
@@ -7,19 +7,17 @@ title: "`r paste('Shinyscreen', packageVersion('shinyscreen'))`"
```{r, context='setup', include='false'}
def_state <- new_state()
-
-def_datafiles <- shinyscreen:::dtable("File"=character(0),
- "tag"=character(0))
-
-def_tags <- shinyscreen:::dtable("tag"=factor(),
- "adduct"=factor(levels=shinyscreen:::DISP_ADDUCTS),
- "set"=factor())
-
-def_state$input$datafiles <- def_datafiles
-def_state$input$tab$tags <- def_tags
+def_datafiles <- shinyscreen:::dtable(File=character(0),
+ tag=character(0))
+def_datatab <- shinyscreen:::dtable("tag"=factor(),
+ "adduct"=factor(levels=shinyscreen:::DISP_ADDUCTS),
+ "set"=factor())
+## def_state$input$tab$tags <- def_datatab
rv_state <- list2rev(def_state)
compl_sets <- eventReactive(rv_state$input$tab$setid,
rv_state$input$tab$setid[,unique(set)])
+## Reactive values to support some of the UI elements.
+## rv_ui <- reactiveValues(datatab=def_tags)
```
@@ -359,6 +357,19 @@ shiny::textInput(inputId = "rep_aut", label = "Report author", value = def_state
shiny::textInput(inputId = "rep_tit", label = "Report title", value = def_state$conf$report$title)
```
+# View compound Lists and Sets {.tabset}
+
+## Compound List
+
+```{r, echo=F}
+DT::dataTableOutput("comp_table")
+```
+
+## Setid Table
+```{r, echo=F}
+DT::dataTableOutput("setid_table")
+```
+
# Extract Data and Prescreen
<details><summary>Extract spectra from data files.</summary>
@@ -389,19 +400,81 @@ ord_asc <- grepl("^-.+",shinyscreen:::DEF_INDEX_SUMM)
ord_asc <- factor(ifelse(ord_asc, "descending", "ascending"),levels = c("ascending","descending"))
def_ord_summ <- shinyscreen:::dtable("Column names"=ord_nms,"Direction"=ord_asc)
+```
-
+```{r, include="false", context='server'}
## reactive functions
-rv_setup_phase <- reactive({
- rv_state$conf$
- state < rev2
-
+rf_compound_input_state <- reactive({
+ sets <- rv_state$conf$compounds$sets
+ lst <- as.list(rv_state$conf$compounds$lists)
+ validate(need(length(lst)>0,
+ message = "Load the compound lists(s) first."))
+ validate(need(nchar(sets)>0,
+ message = "Load the setid table first."))
+ isolate({
+ state <- rev2list(rv_state)
+ m <- load_compound_input(state)
+ ## Side effect! This is because my pipeline logic does not
+ ## work nicely with reactive stuff.
+ rv_state$input$tab$cmpds <- list2rev(m$input$tab$cmpds)
+ rv_state$input$tab$setid <- m$input$tab$setid
+ m
+ })
})
+rf_get_dfiles <- reactive({
+ input$datafiles_b
+ if (input$datafiles_b > 0) {
+ filters <- matrix(c("mzML files", ".mzML",
+ "All files", "*"),
+ 2, 2, byrow = TRUE)
+ mzMLs <- tcltk::tk_choose.files(filters=filters)
+ message("(config) Selected data files: ", paste(mzMLs,collapse = ","))
+ mzMLs
+ } else character(0)
+})
+rf_dfiles_tab <- reactive({
+ mzMLs <- rf_get_dfiles()
+ isolate({oldtab <- data.table::as.data.table(rhandsontable::hot_to_r(input$datafiles))})
+ newf <- setdiff(mzMLs,oldtab$File)
+ nr <- NROW(oldtab)
+ tmp <- if (length(newf)>0) shinyscreen:::dtable(File=newf,tag=paste0('F',(nr+1):(nr + length(newf)))) else shinyscreen:::dtable(File=character(),tag=character())
+ rbind(oldtab,
+ tmp)
+})
+rf_tag_tab <- reactive({
+ state <- rf_compound_input_state()
+ isolate({oldtab <- rhandsontable::hot_to_r(input$datatab)})
+ oldt <- oldtab$tag
+ sets <- compl_sets()
+ sets <- if (length(sets)==1) sets <- c(sets,"invalid") #Just
+ #because
+ #when one
+ #level,
+ #rhandsontable
+ #has issues
+ #displaying
+ #it.
+ otagch <- as.character(oldt)
+ df_tab <- rhandsontable::hot_to_r(input$datafiles)
+ tagl <- df_tab$tag
+ diff <- setdiff(tagl,
+ otagch)
+ if (length(diff)!=0) {
+ tmp <- shinyscreen:::dtable(tag=factor(diff,levels=tagl),
+ adduct=factor(levels = shinyscreen:::DISP_ADDUCTS),
+ set=factor(levels = sets))
+
+ dt <-data.table::as.data.table(rbind(as.data.frame(oldtab),
+ as.data.frame(tmp)))
+ dt[tag %in% df_tab$tag,]
+ } else oldtab
+})
```
+
```{r, include="false", context='server'}
observeEvent(input$project_b,{
@@ -437,35 +510,7 @@ observeEvent(input$extract,{
message("(extract) Config written to ", fn_c_state)
})
-observeEvent(input$datafiles_b, {
- filters <- matrix(c("mzML files", ".mzML",
- "All files", "*"),
- 2, 2, byrow = TRUE)
- mzMLs <- tcltk::tk_choose.files(filters=filters)
- message("(config) Selected data files: ", paste(mzMLs,collapse = ","))
- newf <- setdiff(mzMLs,rv_state$input$datafiles$File)
- nr <- NROW(rv_state$input$datafiles)
- tmp <- if (length(newf)>0) shinyscreen:::dtable(File=newf,tag=paste0('F',(nr+1):(nr + length(newf)))) else shinyscreen:::dtable(File=character(),tag=character())
- rv_state$input$datafiles <- rbind(rv_state$input$datafiles,
- tmp)
-})
-observeEvent(rv_state$input$datafiles,
-{
- oldt <- rv_state$input$tab$tags$tag
- otagch <- as.character(oldt)
- tagl <- rv_state$input$datafiles$tag
-
- diff <- setdiff(tagl,
- otagch)
-
- tmp <- shinyscreen:::dtable(tag=factor(diff,levels=tagl),
- adduct=factor(levels = shinyscreen:::DISP_ADDUCTS),
- set=factor())
-
- rv_state$input$tab$tags <- rbind(rv_state$input$tab$tags,
- tmp)
-})
```
@@ -497,16 +542,51 @@ output$order_summ <- rhandsontable::renderRHandsontable(rhandsontable::rhandsont
output$datafiles <- rhandsontable::renderRHandsontable(
{
- validate(need(NROW(rv_state$input$tab$setid)>0, message = "Please load the setid table first."))
- rhandsontable::rhandsontable(rv_state$input$datafiles,
- width = "50%",height = "25%")
+ res <- if (length(rf_get_dfiles())>0) {
+ rf_dfiles_tab()
+
+ } else def_datafiles
+ rhandsontable::rhandsontable(as.data.frame(res),
+ width = "50%",
+ height = "25%",
+ allowInvalid=F)
})
output$datatab <- rhandsontable::renderRHandsontable(
{
- validate(need(NROW(rv_state$input$datafiles)>0, message = "Please load some data files first."))
- rhandsontable::rhandsontable(rv_state$input$tab$tags,
- stretchH="all")
+ df <- rhandsontable::hot_to_r(input$datafiles)
+ res <- if (NROW(rv_state$input$tab$setid) > 0 &&
+ NROW(df) > 0) rf_tag_tab() else def_datatab
+
+ rhandsontable::rhandsontable(res,stretchH="all",
+ allowInvalid=F)
+})
+
+output$comp_table <- DT::renderDataTable({
+ state <- rf_compound_input_state()
+
+
+ DT::datatable(state$input$tab$cmpds,
+ style = 'bootstrap',
+ class = 'table-condensed',
+ extensions = 'Scroller',
+ options = list(scrollX = T,
+ scrollY = 200,
+ deferRender = T,
+ scroller = T))
+})
+
+output$setid_table <- DT::renderDataTable({
+ state <- rf_compound_input_state()
+
+ DT::datatable(state$input$tab$setid,
+ style = 'bootstrap',
+ class = 'table-condensed',
+ extensions = 'Scroller',
+ options = list(scrollX = T,
+ scrollY = 200,
+ deferRender = T,
+ scroller = T))
})
```