shiny-ui-base, state, app: Export MS2 spectra.

* state.R (encode_ms2_to_line, pack_ms2_w_summ): Functions to pack ms2
data based on selected entries in `summ'.

* app (ms2_spectra_tab_name, ms2_spectra_tab_b): New widgets.

* shiny-ui-base: Added input$ms2_spectra_tab_b observer.

R/shiny-ui-base.R

@@ -1270,6 +1270,17 @@ mk_shinyscreen_server <- function(projects,init) {
             tab2file(rvs$m$out$tab$summ,fn)
         })
 
+        observeEvent(input$ms2_spectra_tab_b,{
+            req(NROW(rvs$m$out$tab$summ)>0L)
+            projdir <- rvs$gui$paths$project
+            fn <- file.path(projdir,input$ms2_spectra_tab_name)
+            shinymsg(paste0("Saving MS2 spectra table to: ",basename(fn)))
+            tab2file(pack_ms2_w_summ(rvs$m$out$tab$summ,
+                                    rvs$m$extr$ms2),
+                     fn)
+            shinymsg("Done saving MS2 spectra table.")
+        })
+
 
         observeEvent(input$plot_brush,{
             xmin <- round(input$plot_brush[["xmin"]],3)

R/state.R

@@ -237,3 +237,18 @@ new_conf <- function() fig_conf(
                            presc_conf(
                                extr_conf(
                                    base_conf())))
+
+encode_ms2_to_line <- function(ms2) {
+    ## ms2 is a data.frame whose first column is mz and the second intensity.
+    paste0(paste(ms2[[1]],ms2[[2]],sep=':'),collapse=';')
+}
+
+
+pack_ms2_w_summ <- function(summ,ms2) {
+    ## Takes summ, finds entries with high quality spectra and subsets ms2 based on that.
+
+    ## Take the columns we need from summ.
+    x = summ[ms2_sel==T,.SD,.SDcols=c(key(summ),"mz","SMILES","Formula","Name")]
+    mrg_keys = c(intersect(key(ms2),key(summ)),"an")
+    ms2[x,.(mz=i.mz,ms2_spectrum=encode_ms2_to_line(.SD[,c("mz","intensity")])),on=mrg_keys,by=.EACHI]
+}

inst/rmd/app.Rmd

@@ -733,6 +733,11 @@ textInput("summ_name",
           label="Summary table name",
           value="summary.csv")
 actionButton("summ_tab_b", "Save summary table")
+
+textInput("ms2_spectra_tab_name",
+          label="Table of MS2 spectra",
+          value="ms2_spectra_table.csv")
+actionButton("ms2_spectra_tab_b", "Save MS2 spectra table")
 ```
 
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