The output `print_spec_tab' now adapted to new data model.

* shiny-ui-base(gen_cindex, gen_summ_subset): Adapted. Function
`gen_cindex' now returns less confusing output.

* plotting(get_data_from_key): Argument `outcols' now has a default
NULL value.

R/plotting.R

@@ -194,7 +194,7 @@ mk_logic_exp <- function(rest,sofar=NULL) {
 }
 
 
-get_data_from_key <- function(db,tab,kvals,outcols) {
+get_data_from_key <- function(db,tab,kvals,outcols=NULL) {
 
     ## Ensure only names that exist in cat are used in selection. Or,
     ## should we not do this?
@@ -209,7 +209,8 @@ get_data_from_key <- function(db,tab,kvals,outcols) {
     ## Get precids.
     mztab = db$precursors[cattab,on="catid"]
     outnames = union(valid_names,outcols)
-    tab[mztab,on="precid"][,..outnames]
+    res = tab[mztab,on="precid"]
+    if (!is.null(outcols)) res[,..outnames] else res
     
 }
 

R/shiny-state.R

@@ -495,11 +495,11 @@ gen_cindex <- function(summ,sorder,cols = CINDEX_COLS,by. = CINDEX_BY) {
     xsumm <- summ[,..allc]
     setnames(xsumm,old="ms1_rt",new="rt",skip_absent=T)
     res <- xsumm[,.SD[max(qlt_ms1)==qlt_ms1][max(qlt_ms2)==qlt_ms2],by=by.]
-    res <- res[,c("mz","rt","Name","qlt_ms1","qlt_ms2"):=.(first(mz),
-                                                         first(mean(rt)),
-                                                         first(Name),
-                                                         first(qlt_ms1),
-                                                         first(qlt_ms2)),
+    res <- res[,c("mz","rt","Name","qlt_ms1","qlt_ms2"):=.(mean(mz,na.rm=T),
+                                                           mean(rt,na.rm=T),
+                                                           first(Name),
+                                                           max(qlt_ms1,na.rm=T),
+                                                           max(qlt_ms2,na.rm=T)),
                by=by.]
     res <- res[,unique(.SD),by=by.]
    
@@ -518,7 +518,11 @@ gen_cindex <- function(summ,sorder,cols = CINDEX_COLS,by. = CINDEX_BY) {
         ord[ind] <- -1L
     }
     if (length(sorder)>0) setorderv(res,cols=sorder,order=ord)
-    setnames(res,old="rt",new="rt(ms1)")
+
+    ## Remove confusing columns.
+    res[,c("rt","mz"):=NULL]
+    res[,c("qlt_ms1","qlt_ms2"):=.(signif(100*qlt_ms1/10.,3),signif(100*qlt_ms2/10.,3))]
+    setnames(res,c("qlt_ms1","qlt_ms2"),c("best score (ms1)","best score (ms2)"))
     res
 }
 
@@ -554,9 +558,9 @@ get_cindex_kval <- function(cindex,row,key) {
     res
 }
 
-get_summ_subset <- function(summ,ptab,paritem,kvals) {
+get_summ_subset <- function(db,summ,ptab,paritem,kvals) {
     select <- ptab[item==(paritem)]
-    tab <- get_data_from_key(summ,kvals)[select,nomatch=NULL,on=key(ptab)]
+    tab <- get_data_from_key(db=db,tab=summ,kvals=kvals)[select,nomatch=NULL,on=key(ptab)]
     if ("scan.1" %in% names(tab)) tab[,scan.1:=NULL] #TODO: This is
                                                  #probably a lousy
                                                  #hack.

R/shiny-ui-base.R

@@ -760,7 +760,8 @@ mk_shinyscreen_server <- function(projects,init) {
             kvals = req(rf_get_cindex_kval())
             ptab = rf_get_cindex_parents()
             if (isTruthy(parent)) {
-                get_summ_subset(summ=summ,
+                get_summ_subset(db=rvs$m$db,
+                                summ=summ,
                                 ptab=ptab,
                                 paritem=parent,
                                 kvals=kvals)
@@ -1774,8 +1775,9 @@ mk_shinyscreen_server <- function(projects,init) {
                 #it.
                 key = unique(c(names(allval)[names(allval) %in% BASE_KEY_MS2],"scan"))
                 kval2 = allval[key]
-                spec = get_data_from_key(ms2,kval2)[,.(mz,intensity)]
-                ## as.character(lapply(1L:NROW(spec),function(nr) paste0(spec[nr,mz]," ",spec[nr,intensity])))
+                ## Only precid and scan can be used for selection in spectra.
+                kval2 = as.data.table(kval2[c("precid","scan")])
+                spec = rvs$m$db$extr$spectra[kval2,.(mz,intensity),on=.(precid,scan)]
                 print(as.data.frame(spec),row.names=F)
                 
             } else {