...

R/mix.R

@@ -194,7 +194,19 @@ gen_summ <- function(comp,qa_ms1,qa_ms2) {
     summ$Comments<-""
     data.table::setkeyv(summ,DEF_KEY_SUMM)
     data.table::setcolorder(summ,SUMM_COLS)
+
+    ## Quality scores for ms1 and ms2.
+    summ[,qa_ms1 := Map(function(m1,m2,m3) { m1*5L + m2*3L + m3*2L},
+                        as.integer(qa_ms1_exists),
+                        as.integer(qa_ms1_above_noise),
+                        as.integer(qa_ms1_good_int))]
+    summ[,qa_ms2 := Map(function(m1,m2,m3) { m1*5L + m2*3L + m3*2L},
+                        as.integer(qa_ms2_exists),
+                        as.integer(qa_ms2_near),
+                        as.integer(qa_ms2_good_int))]
+
     summ
+    
 }
 pp_touch_q<-function(summ) {
     ## Returns indices that are ok to be auto processed.

R/resources.R

@@ -285,3 +285,4 @@ DFILES_LIST_PATT <- ".*\\.mz[Mm][Ll]$"
 
 CINDEX_BY <- c("set","adduct","tag","ID")
 CINDEX_COLS <- c("mz", "ms1_rt", "Formula","Name")
+ARRANGE_CHOICES <- c(NA_character_,"quality","set", "adduct", "tag", "mz", "rt") 

R/shiny-state.R

@@ -335,8 +335,9 @@ pre_setup_val_block <- function(gui) {
     T
 }
 
-gen_cindex <- function(summ,cols = CINDEX_COLS,by. = CINDEX_BY) {
+gen_cindex <- function(summ,cols = CINDEX_COLS,by. = CINDEX_BY, sort=character(0)) {
     allc <- c(by.,cols)
-    summ[,first(.SD),by=by.][,..allc]
+    res <- summ[,first(.SD),by=by.][,..allc]
+    
 
 }

R/shiny-ui-base.R

@@ -706,8 +706,27 @@ mk_shinyscreen_server <- function(projects,init) {
 
         rf_get_cindex <- eventReactive(rvs$status$is_qa_stat,{
             summ <- req(rvs$m$out$tab$summ)
-            ## simple_style_dt(gen_cindex(summ))
-            gen_cindex(summ)
+            if (NROW(summ)>0L) {
+                s1 <- input$sort1
+                s2 <- input$sort2
+                s3 <- input$sort3
+                s4 <- input$sort4
+                sortorder <- unique(c(s1,s2,s3,s4))
+                message("----")
+                message(paste0(sortorder,collapse=','))
+                wna <- which(is.na(sortorder)); if (length(wna)>0L) sortorder <- sortorder[-wna]
+                message(paste0(sortorder,collapse=','))
+                quality <- which("quality"==sortorder)
+                if (length(quality)>0L) {
+                    pre <- head(sortorder,quality-1L)
+                    post <- tail(sortorder,quality+1L)
+                    sortorder <- c(pre,"qa_ms1","qa_ms2",post)
+                }
+                message(paste0(sortorder,collapse=','))
+                setorderv(gen_cindex(summ),cols=sortorder)
+            } else {
+                NULL
+            }
         })
 
         
@@ -1132,8 +1151,7 @@ mk_shinyscreen_server <- function(projects,init) {
         output$cindex <- DT::renderDT({
             tab <- rf_get_cindex()
             validate(need(NROW(tab)>0L,message="Need to prescreen, first."))
-            print(names(tab))
-            simple_style_dt(tab)
+            styled_dt(tab)
         })
 
         

inst/rmd/app.Rmd

@@ -663,6 +663,23 @@ selectInput("cindex_switch_ms2", label="Select MS2 to show", width="30%", choice
 
 <div>
 ### Arrange
+
+```{r, echo=F} 
+selectInput("sort1",label="Group the compound index first by", choices=ARRANGE_CHOICES, selected="quality")
+```
+
+```{r, echo=F} 
+selectInput("sort2",label="then", choices=ARRANGE_CHOICES, selected="set")
+```
+
+```{r, echo=F} 
+selectInput("sort3",label="then", choices=ARRANGE_CHOICES, selected="adduct")
+```
+
+```{r, echo=F} 
+selectInput("sort4",label="and finally", choices=ARRANGE_CHOICES, selected="tag")
+```
+
 </div> <!-- Arrange -->
 
 <div>