Merge pull request #77 from khabatv/master

changing prettynum, digits = 0 to 1
ipb-halle · Mar 10, 2024 · 625e593 · 625e593
2 parents 87fd457 + 6769831
commit 625e593
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Showing 5 changed files with 13 additions and 13 deletions.
diff --git a/R/DataProcessing.R b/R/DataProcessing.R
@@ -1477,7 +1477,7 @@ getTableFromPrecursorSet <- function(dataList, precursorSet){
   featureMatrix <- data.frame(as.matrix(dataList$featureMatrix[precursorSet, featureIndeces, drop = FALSE]))
   rownames(featureMatrix) <- dataList$precursorLabels[precursorSet]
   colnames(featureMatrix) <- colnames(dataList$featureMatrix)[featureIndeces]
-  featureMatrix <- format(x = featureMatrix, digits = 0, nsmall = 4)
+  featureMatrix <- format(x = featureMatrix, digits = 1, nsmall = 4)
   if(length(featureIndeces) > 0){
     featureMatrix[featureMatrix=="0.0000"] <- "-"
     featureMatrix[featureMatrix=="1.0000"] <- "1"

diff --git a/R/FragmentMatrixFunctions.R b/R/FragmentMatrixFunctions.R
@@ -1644,7 +1644,7 @@ convertToProjectFile2 <- function(filePeakMatrix,
   if(isGC){
     ## round GC mzs to integer
     for(spectrumIdx in seq_len(length(spectraList))){
-      spectraList[[spectrumIdx]]$ms2Peaks_mz <- round(x = spectraList[[spectrumIdx]]$ms2Peaks_mz, digits = 0)
+      spectraList[[spectrumIdx]]$ms2Peaks_mz <- round(x = spectraList[[spectrumIdx]]$ms2Peaks_mz, digits = 1)
     }
   }
 

diff --git a/R/Plots.R b/R/Plots.R
@@ -2154,7 +2154,7 @@ calcPlotMS2 <- function(dataList, fragmentsX = NULL, fragmentsY = NULL, fragment
   if(length(dataX) > 0){
     ## axis with the individual fragment m/z's (ticks, labels)
     axis(side = 1, at = dataX, labels = FALSE, las = 2)
-    axis(side = 1, at = tickPositions, labels = format(x = dataX, digits = 0, nsmall = 4), las = 2, tick = FALSE)
+    axis(side = 1, at = tickPositions, labels = format(x = dataX, digits = 1, nsmall = 4), las = 2, tick = FALSE)
 
     ## sticks
     points(x = dataX, y = dataY, col = nodeColors, type = "h", lwd=4)
@@ -4961,7 +4961,7 @@ plotFragments <- function(masses, numberOfFragments, colors = NULL, numberOfPrec
   #axis(side = 1, at = dataList$ms2_masses, labels = dataList$ms2_masses, las = 2, tick = TRUE, col = colors)
   #for(i in 1:length(dataList$ms2_masses))
   for(i in dataOrder)
-    axis(side = 1, at = masses[[i]], labels = format(x = masses[[i]], digits = 0, nsmall = 4), las = 2, tick = TRUE, col.axis = colors[[i]])
+    axis(side = 1, at = masses[[i]], labels = format(x = masses[[i]], digits = 1, nsmall = 4), las = 2, tick = TRUE, col.axis = colors[[i]])
 
   points(x = masses[dataOrder], y = numberOfFragments[dataOrder], col = colors[dataOrder], type = "h", lwd=4)
   #points(x = masses[dataOrder], y = numberOfFragments[dataOrder], col = colors[dataOrder], pch=19, cex=1.)
@@ -5040,7 +5040,7 @@ plotFragments2 <- function(masses, numberOfFragments, numberOfPrecursors, xInter
   #axis(side = 1, at = masses, labels = masses, las = 2, tick = TRUE, col = colors)
   #for(i in 1:length(masses))
   for(i in dataOrder)
-    axis(side = 1, at = masses[[i]], labels = format(x = masses[[i]], digits = 0, nsmall = 4), las = 2, tick = TRUE, col.axis = colors[[i]])
+    axis(side = 1, at = masses[[i]], labels = format(x = masses[[i]], digits = 1, nsmall = 4), las = 2, tick = TRUE, col.axis = colors[[i]])
 
   points(x = masses[dataOrder], y = numberOfFragments[dataOrder], col = colors[dataOrder], type = "h", lwd=4)
   #points(x = masses[dataOrder], y = numberOfFragments[dataOrder], col = colors[dataOrder], pch=19, cex=1.)
@@ -5161,12 +5161,12 @@ calcPlotSpectrumVsClass_big <- function(masses_spec, intensity_spec, colors_spec
 
   ## axis with the individual fragment m/z's (ticks, labels)
   axis(side = 1, at = masses_spec, labels = FALSE, las = 2)
-  axis(side = 1, at = masses_spec[-these], labels = format(x = masses_spec[-these], digits = 0, nsmall = 4), las = 2, tick = FALSE, col.axis = "grey")
+  axis(side = 1, at = masses_spec[-these], labels = format(x = masses_spec[-these], digits = 1, nsmall = 4), las = 2, tick = FALSE, col.axis = "grey")
   if(length(these) == 1){
     if(these != length(masses_spec)+1)
-      axis(side = 1, at = masses_spec[ these], labels = format(x = masses_spec[ these], digits = 0, nsmall = 4), las = 2, tick = FALSE, col.axis = "black")
+      axis(side = 1, at = masses_spec[ these], labels = format(x = masses_spec[ these], digits = 1, nsmall = 4), las = 2, tick = FALSE, col.axis = "black")
   } else {
-    axis(side = 1, at = masses_spec[ these], labels = format(x = masses_spec[ these], digits = 0, nsmall = 4), las = 2, tick = FALSE, col.axis = "black")
+    axis(side = 1, at = masses_spec[ these], labels = format(x = masses_spec[ these], digits = 1, nsmall = 4), las = 2, tick = FALSE, col.axis = "black")
   }
 
   ## sticks

diff --git a/inst/MetFamily/app_files/server_guiMs2plot.R b/inst/MetFamily/app_files/server_guiMs2plot.R
@@ -92,7 +92,7 @@ obsMS2hover <- observeEvent(input$plotMS2_hover, {
       print(paste("update output$information"))
       paste(
         "Fragment with m/z = ", ms2PlotValues$fragmentListClicked$fragmentMasses[[minimumIndex]], 
-        " and (average) abundance = ", format(x = ms2PlotValues$fragmentListClicked$fragmentAbundances[[minimumIndex]], digits = 0, nsmall = 4), 
+        " and (average) abundance = ", format(x = ms2PlotValues$fragmentListClicked$fragmentAbundances[[minimumIndex]], digits = 1, nsmall = 4), 
         " is present in ", numberOfPrecursors, " MS/MS spectra",
         "\nand has a cluster-discriminating power of ", format(x = ms2PlotValues$fragmentListClicked$fragmentDiscriminativity[[minimumIndex]]*100, digits = 3, nsmall = 2), "%.", 
         sep = ""
@@ -164,7 +164,7 @@ output$plotMS2_hover_info <- renderUI({
   #  print(paste("update output$information"))
   #  paste(
   #    "Fragment with m/z = ", ms2PlotValues$fragmentListClicked$fragmentMasses[[minimumIndex]], 
-  #    " and (average) abundance = ", format(x = ms2PlotValues$fragmentListClicked$fragmentAbundances[[minimumIndex]], digits = 0, nsmall = 4), 
+  #    " and (average) abundance = ", format(x = ms2PlotValues$fragmentListClicked$fragmentAbundances[[minimumIndex]], digits = 1, nsmall = 4), 
   #    " is present in ", numberOfPrecursors, " MS/MS spectra",
   #    "\nand has a cluster-discriminating power of ", format(x = ms2PlotValues$fragmentListClicked$fragmentDiscriminativity[[minimumIndex]]*100, digits = 3, nsmall = 2), "%.", 
   #    sep = ""
@@ -173,7 +173,7 @@ output$plotMS2_hover_info <- renderUI({
 
   fragmentMz <- ms2PlotValues$fragmentListClicked$fragmentMasses[[minimumIndex]]
   fragmentMzS <- format(x = fragmentMz, nsmall = 4)
-  intensityS <- format(x = ms2PlotValues$fragmentListClicked$fragmentAbundances[[minimumIndex]], digits = 0, nsmall = 4)
+  intensityS <- format(x = ms2PlotValues$fragmentListClicked$fragmentAbundances[[minimumIndex]], digits = 1, nsmall = 4)
   cdpS <- format(x = ms2PlotValues$fragmentListClicked$fragmentDiscriminativity[[minimumIndex]]*100, digits = 3, nsmall = 2)
 
   info <- paste(

diff --git a/inst/MetFamily/app_files/server_guiTabHca.R b/inst/MetFamily/app_files/server_guiTabHca.R
@@ -626,7 +626,7 @@ obsHeatmaphover <- observeEvent(input$plotHeatmap_hover, {
 
   #################################################
   ## info
-  treeLeafIndex2 <- as.numeric(format(x = hoverX, digits = 0))
+  treeLeafIndex2 <- as.numeric(format(x = hoverX, digits = 1))
   treeLeafIndex  <- clusterDataList$cluster$order[[treeLeafIndex2]]
   precursorIndex <- filterHca$filter[[treeLeafIndex]]
 
@@ -698,7 +698,7 @@ output$plotHeatmap_hover_info <- renderUI({
     return(NULL)
 
   #################################################
-  treeLeafIndex2 <- as.numeric(format(x = hoverX, digits = 0))
+  treeLeafIndex2 <- as.numeric(format(x = hoverX, digits = 1))
   treeLeafIndex  <- clusterDataList$cluster$order[[treeLeafIndex2]]
   precursorIndex <- filterHca$filter[[treeLeafIndex]]