filterSOI bugfixing

Fix problem with GUI variable names #11 Add checks to filterSOI to raise a warning if no SOIs remain after each filtering step
RogerGinBer · Jan 5, 2022 · d372d48 · d372d48
1 parent 10189ac
commit d372d48
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Showing 2 changed files with 21 additions and 8 deletions.
diff --git a/R/SOI_functions.R b/R/SOI_functions.R
@@ -707,7 +707,12 @@ setMethod("filterSOI", signature = c("RHermesExp", "numeric", "ANY", "ANY", "ANY
         ##Filter by maximum intensity
         intense_enough <- which(soilist$MaxInt > minint)
         soilist <- soilist[intense_enough, ]
-
+        if(nrow(soilist) == 0){
+            warning("No SOIs remaining after filtering by intensity. ",
+                    "Aborting filter")
+            return(struct)
+        }
+
         ##Filter by isotopic fidelity
         if (isofidelity) {
             # Isotopic elution similarity
@@ -717,6 +722,12 @@ setMethod("filterSOI", signature = c("RHermesExp", "numeric", "ANY", "ANY", "ANY
             soilist <- soilist[good, ]
             with_isos <- intense_enough[good]
 
+            if(nrow(soilist) == 0){
+                warning("No SOIs remaining after filtering by isotopic elution",
+                        " similarity. Aborting filter")
+                return(struct)
+            }
+
             # Isotopic pattern similarity
             message("Calculating isotopic fidelity metrics:")
             isodata <- lapply(with_isos, plotFidelity, struct = struct,
@@ -726,6 +737,12 @@ setMethod("filterSOI", signature = c("RHermesExp", "numeric", "ANY", "ANY", "ANY
             soilist$isofidelity <- cos
             soilist <- soilist[cos > minscore, ]
 
+            if(nrow(soilist) == 0){
+                warning("No SOIs remaining after filtering by isotopic ",
+                        "fidelity. Aborting filter")
+                return(struct)
+            }
+
             rtmargin <- 20
             # Removing confirmed isotopic signals
             soilist <- soilist[order(-soilist$MaxInt), ]

diff --git a/inst/app/SOI_UI.R b/inst/app/SOI_UI.R
@@ -236,8 +236,8 @@ SOIServer <- function(id, struct){
                       style = "margin-top: 5px"
                       ))
             ),
-            numericInput(ns("numericval"), label = "Minimum SOI intensity", value = 0,
-                         min = 0, max = 1e5, step = 1000),
+            numericInput(ns("minfilter"), label = "Minimum SOI intensity", value = 0,
+                         min = 0, max = 5e5, step = 1000),
             fluidRow(
               actionButton(inputId = ns("soiClean"), label = "Start SOI Cleaning",
                            style = "text-align: center; background-color: #4d4263; color: #F0F0F0"),
@@ -247,11 +247,7 @@ SOIServer <- function(id, struct){
 
       }, ignoreNULL = TRUE,ignoreInit = TRUE, priority = 100)
 
-      observeEvent(input$minfilter,{
-        updateNumericInput(session, "numericval", value = input$minfilter)
-      })
-
-      observeEvent(input$soiClean,{
+      observeEvent(input$soiClean, {
         struct$dataset <- filterSOI(struct$dataset,
                             as.numeric(input$soiChoices),
                             as.numeric(input$minfilter),