- info_state manager uses switch

- clean up
- set smoothHalfWindowSize to a more reasonable value

functions/doFitCurve.R

@@ -1,5 +1,3 @@
-
-
 doFitCurve <- function(appData, spec, input) {
 
   #res <- NULL
@@ -24,6 +22,5 @@ doFitCurve <- function(appData, spec, input) {
     cat("fitCurve returned null.\n")
   }
 
-
   return(res)
 }

functions/infoStateMassageHandler.R

@@ -1,44 +1,46 @@
 infoStateMassageHandler <- function(info_state, output) {
-  if (info_state == "inital") {
-    output$info1 <- renderText("Please select\na folder.")
-    output$info2 <- renderText("")
-    output$info3 <- renderText("")
-  }
-  if (info_state == "dir_set") {
-    output$info1 <- renderText("Selected:")
-    output$info2 <- renderText(appData$selected_dir)
-    output$info3 <- renderText("Press load button.")
-  }
-  if (info_state == "loaded") {
-    output$info1 <- renderText("Loaded:")
-    output$info2 <- renderText(appData$selected_dir)
-    output$info3 <- renderText("Press process button.")
-  }
-  if (info_state == "processed") {
-    output$info1 <- renderText(("Dataset:"))
-    output$info2 <- renderText(appData$selected_dir)
-    output$info3 <- renderText("Changed settings apply after re-processing.")
-  }
-  if (info_state == "fitErrorRecal") {
-    output$info1 <- renderText(("Dataset:"))
-    output$info2 <- renderText(appData$selected_dir)
-    output$info3 <- renderText("Could not be processed. Wrong lock-mass?")
-  }
-  if (info_state == "fitErrorNorm") {
-    output$info1 <- renderText(("Dataset:"))
-    output$info2 <- renderText(appData$selected_dir)
-    output$info3 <- renderText("Could not be processed. Wrong normalization-mass?")
-  }
-  if (info_state == "RefMzError") {
-    output$info1 <- renderText(("Dataset:"))
-    output$info2 <- renderText(appData$selected_dir)
-    output$info3 <- renderText("Could not be processed. Increase tolerance?")
-  }
-  if (info_state == "fitErrorOther") {
-    output$info1 <- renderText(("Dataset:"))
-    output$info2 <- renderText(appData$selected_dir)
-    output$info3 <- renderText("Could not be processed. Unkown error.\n")
-  }
+    switch(info_state,
+     "inital" = {
+      output$info1 <- renderText("Please select\na folder.")
+      output$info2 <- renderText("")
+      output$info3 <- renderText("")
+    },
+     "dir_set" = {
+      output$info1 <- renderText("Selected:")
+      output$info2 <- renderText(appData$selected_dir)
+      output$info3 <- renderText("Press load button.")
+    },
+    "loaded" = {
+      output$info1 <- renderText("Loaded:")
+      output$info2 <- renderText(appData$selected_dir)
+      output$info3 <- renderText("Press process button.")
+    },
+    "processed" = {
+      output$info1 <- renderText(("Dataset:"))
+      output$info2 <- renderText(appData$selected_dir)
+      output$info3 <- renderText("Changed settings apply after re-processing.")
+    },
+    "fitErrorRecal" = {
+      output$info1 <- renderText(("Dataset:"))
+      output$info2 <- renderText(appData$selected_dir)
+      output$info3 <- renderText("Could not be processed. Wrong lock-mass?")
+    },
+    "fitErrorNorm" = {
+      output$info1 <- renderText(("Dataset:"))
+      output$info2 <- renderText(appData$selected_dir)
+      output$info3 <- renderText("Could not be processed. Wrong normalization-mass?")
+    },
+    "RefMzError" = {
+      output$info1 <- renderText(("Dataset:"))
+      output$info2 <- renderText(appData$selected_dir)
+      output$info3 <- renderText("Could not be processed. Increase tolerance?")
+    },
+    "fitErrorOther" = {
+      output$info1 <- renderText(("Dataset:"))
+      output$info2 <- renderText(appData$selected_dir)
+      output$info3 <- renderText("Could not be processed. Unkown error.\n")
+    }
+  )
 
   return(output)
 }

functions/loadAllFunctions.R

@@ -18,7 +18,6 @@ loadAllFunctions <- function() {
   source("functions/createDataTable.R")
   source("functions/storeResults.R")
   source("functions/emptyAppDataObject.R")
-  source("functions/prepareVi.R")
   source("functions/detectOutliers.R")
 
 }

functions/plotFunctions.R

@@ -101,44 +101,6 @@ loadingsPlot <- function(pca, pc, simple = TRUE, n = 10) {
   return(p)
 }
 
-glmRegPlot <- function(model, penalty) {
-  p <- getModelFit(model, penalty) %>%
-    predict(model$prepData) %>%
-    mutate(truth = pull(model$prepData, conc)) %>%
-    ggplot(aes(x = .pred, y = truth)) +
-    geom_point(alpha = 0.5) +
-    geom_smooth(method = "lm") +
-    ggpubr::stat_regline_equation(aes(label = paste0("R2adj.=", ..adj.rr..))) +
-    coord_obs_pred() +
-    labs(x = "Log-predicted conc.",
-         y = "Log-true conc.")
-
-  return(p)
-}
-
-viPlot <- function(vi) {
-  NumNonZeoroCoef <- vi %>%
-    filter(Importance > 0) %>%
-    pull(Importance) %>%
-    length()
-
-  p <- vi  %>%
-    arrange(desc(Importance)) %>%
-    slice_head(n = 20) %>%
-    mutate(Variable = round(readr::parse_number(Variable), 3)) %>%
-    mutate(imp = ifelse(Sign == "POS", Importance, -Importance)) %>%
-    mutate(Variable = fct_reorder(as.factor(Variable), imp)) %>%
-    ggplot(aes(x = Variable, y = imp, fill = Sign)) +
-    geom_col() +
-    geom_text(aes(x = 1, y = 0, label = paste0("#-features =", NumNonZeoroCoef))) +
-    coord_flip() +
-    theme(legend.position = "none") +
-    labs(x = "m/z",
-         y = "Variable importance")
-
-  return(p)
-}
-
 plateMapPlot <- function(appData,
                          stat = c("Concentration",
                                   "Total Peak Intensity",

functions/preprocessFunction.R

@@ -2,7 +2,7 @@ preprocess <- function(spectra,
                        smooth,
                        rmBaseline,
                        sqrtTransform = FALSE,
-                       smoothHalfWindowSize = 3,
+                       smoothHalfWindowSize = 20,
                        smoothMethod = "SavitzkyGolay",
                        rmBlMethod = "TopHat",
                        SNR,

req.txt

@@ -4,7 +4,6 @@ tibble
 tidyr
 ggplot2
 purrr
-readr
 stringr
 forcats
 shinyFiles