update fsx for hp

docs/NB01b_Plant_Systems_Biology.fsx

@@ -73,10 +73,10 @@ Now, let's get started by loading the required libraries first.
 *)
 
 #r "nuget: FSharp.Stats, 0.4.3"
-#r "nuget: Plotly.NET, 2.0.0-preview.16"
+#r "nuget: Plotly.NET, 4.2.0"
 
 #if IPYNB
-#r "nuget: Plotly.NET.Interactive, 2.0.0-preview.16"
+#r "nuget: Plotly.NET.Interactive, 4.2.0"
 #endif // IPYNB
 
 open System
@@ -299,8 +299,8 @@ let fittedValuesGompertz =
 // combine the raw data and the fit into one chart
 let fittedChartGompertz = 
     [
-        example_Chart_2      |> Chart.withTraceName "raw data"
-        fittedValuesGompertz |> Chart.withTraceName "gompertz model"
+        example_Chart_2      |> Chart.withTraceInfo "raw data"
+        fittedValuesGompertz |> Chart.withTraceInfo "gompertz model"
     ]
     |> Chart.combine
 

docs/NB02b_Digestion_and_mass_calculation.fsx

@@ -34,11 +34,11 @@ Amino acid composition of the proteome is simply counting each amino acid occurr
 
 #r "nuget: BioFSharp, 2.0.0-beta5"
 #r "nuget: BioFSharp.IO, 2.0.0-beta5"
-#r "nuget: Plotly.NET, 2.0.0-preview.16"
-#r "nuget: BIO-BTE-06-L-7_Aux, 0.0.9"
+#r "nuget: Plotly.NET, 4.2.0"
+#r "nuget: BIO-BTE-06-L-7_Aux, 0.0.10"
 
 #if IPYNB
-#r "nuget: Plotly.NET.Interactive, 2.0.0-preview.16"
+#r "nuget: Plotly.NET.Interactive, 4.2.0"
 #endif // IPYNB
 
 open Plotly.NET
@@ -165,7 +165,7 @@ let chartDigestedProteins =
     |> Array.filter (fun x -> x < 3000.)
     // visualize distribution of all peptide masses < 3000 Da
     |> fun masses -> Chart.Histogram(data = masses, orientation = StyleParam.Orientation.Vertical, NBinsX = 100)
-    |> Chart.withXAxisStyle (title = "Mass [Da]", MinMax = (0., 3000.))
+    |> Chart.withXAxisStyle (TitleText = "Mass [Da]", MinMax = (0., 3000.))
     |> Chart.withYAxisStyle "Count"
 
 chartDigestedProteins
@@ -197,7 +197,7 @@ let chartDigestedPeptideMasses =
     |> Array.map (fun ucMass -> Mass.toMZ ucMass 2.)
     |> Array.filter (fun x -> x < 3000.)
     |> fun masses -> Chart.Histogram(data = masses, orientation = StyleParam.Orientation.Vertical, NBinsX=100)
-    |> Chart.withXAxisStyle (title = "m/z", MinMax = (0., 3000.))
+    |> Chart.withXAxisStyle (TitleText = "m/z", MinMax = (0., 3000.))
     |> Chart.withYAxisStyle "Count"
 
 chartDigestedPeptideMasses

docs/NB02c_Isotopic_distribution.fsx

@@ -36,10 +36,10 @@ individual elements (Rockwood et al. 1995), or rely on dynamic programming (Snid
 
 #r "nuget: BioFSharp, 2.0.0-beta5"
 #r "nuget: BioFSharp.IO, 2.0.0-beta5"
-#r "nuget: Plotly.NET, 2.0.0-preview.16"
+#r "nuget: Plotly.NET, 4.2.0"
 
 #if IPYNB
-#r "nuget: Plotly.NET.Interactive, 2.0.0-preview.16"
+#r "nuget: Plotly.NET.Interactive, 4.2.0"
 #endif // IPYNB
 
 open Plotly.NET

docs/NB03a_Retention_time_and_scan_time.fsx

@@ -29,11 +29,11 @@ As always, we start by loading our famous libraries.
 #r "nuget: FSharp.Stats, 0.4.3"
 #r "nuget: BioFSharp, 2.0.0-beta5"
 #r "nuget: BioFSharp.IO, 2.0.0-beta5"
-#r "nuget: Plotly.NET, 2.0.0-preview.16"
-#r "nuget: BIO-BTE-06-L-7_Aux, 0.0.9"
+#r "nuget: Plotly.NET, 4.2.0"
+#r "nuget: BIO-BTE-06-L-7_Aux, 0.0.10"
 
 #if IPYNB
-#r "nuget: Plotly.NET.Interactive, 2.0.0-preview.16"
+#r "nuget: Plotly.NET.Interactive, 4.2.0"
 #endif // IPYNB
 
 open BioFSharp

docs/NB03c_Centroidisation.fsx

@@ -25,12 +25,12 @@ explained under quantification in the following section.
 
 #r "nuget: BioFSharp, 2.0.0-beta5"
 #r "nuget: BioFSharp.IO, 2.0.0-beta5"
-#r "nuget: Plotly.NET, 2.0.0-preview.16"
+#r "nuget: Plotly.NET, 4.2.0"
 #r "nuget: BioFSharp.Mz, 0.1.5-beta"
-#r "nuget: BIO-BTE-06-L-7_Aux, 0.0.9"
+#r "nuget: BIO-BTE-06-L-7_Aux, 0.0.10"
 
 #if IPYNB
-#r "nuget: Plotly.NET.Interactive, 2.0.0-preview.16"
+#r "nuget: Plotly.NET.Interactive, 4.2.0"
 #endif // IPYNB
 
 open Plotly.NET

docs/NB04a_Fragmentation_for_peptide_identification.fsx

@@ -42,11 +42,11 @@ These losses do not change the charge of the ions and are observable as natural
 
 #r "nuget: BioFSharp, 2.0.0-beta5"
 #r "nuget: BioFSharp.IO, 2.0.0-beta5"
-#r "nuget: Plotly.NET, 2.0.0-preview.16"
+#r "nuget: Plotly.NET, 4.2.0"
 #r "nuget: BioFSharp.Mz, 0.1.5-beta"
 
 #if IPYNB
-#r "nuget: Plotly.NET.Interactive, 2.0.0-preview.16"
+#r "nuget: Plotly.NET.Interactive, 4.2.0"
 #endif // IPYNB
 
 open Plotly.NET

docs/NB04b_Peptide_Identification.fsx

@@ -98,12 +98,12 @@ Matching a measured spectrum against chlamy database
 
 #r "nuget: BioFSharp, 2.0.0-beta4"
 #r "nuget: BioFSharp.IO, 2.0.0-beta4"
-#r "nuget: Plotly.NET, 2.0.0-preview.16"
+#r "nuget: Plotly.NET, 4.2.0"
 #r "nuget: BioFSharp.Mz, 0.1.5-beta"
-#r "nuget: BIO-BTE-06-L-7_Aux, 0.0.9"
+#r "nuget: BIO-BTE-06-L-7_Aux, 0.0.10"
 
 #if IPYNB
-#r "nuget: Plotly.NET.Interactive, 2.0.0-preview.16"
+#r "nuget: Plotly.NET.Interactive, 4.2.0"
 #endif // IPYNB
 
 open Plotly.NET

docs/NB05a_Quantification.fsx

@@ -90,16 +90,16 @@ Let’s start and extract a XIC…
 #r "nuget: FSharp.Stats, 0.4.3"
 #r "nuget: BioFSharp, 2.0.0-beta5"
 #r "nuget: BioFSharp.IO, 2.0.0-beta5"
-#r "nuget: Plotly.NET, 2.0.0-preview.16"
+#r "nuget: Plotly.NET, 4.2.0"
 #r "nuget: System.Data.SQLite, 1.0.113.7"
 #r "nuget: BioFSharp.Mz, 0.1.5-beta"
 #r "nuget: MzIO, 0.1.1"
 #r "nuget: MzIO.SQL, 0.1.4"
 #r "nuget: MzIO.Processing, 0.1.2"
-#r "nuget: BIO-BTE-06-L-7_Aux, 0.0.9"
+#r "nuget: BIO-BTE-06-L-7_Aux, 0.0.10"
 
 #if IPYNB
-#r "nuget: Plotly.NET.Interactive, 2.0.0-preview.16"
+#r "nuget: Plotly.NET.Interactive, 4.2.0"
 #endif // IPYNB
 
 open Plotly.NET
@@ -253,7 +253,7 @@ let quantifiedAreaChart =
         Chart.SplineArea(quantifiedArea, Name = "quantified XIC")
     ]
     |> Chart.combine
-    |> Chart.withXAxisStyle (title = "Retention Time", MinMax = (51.,58.))
+    |> Chart.withXAxisStyle (TitleText = "Retention Time", MinMax = (51.,58.))
     |> Chart.withYAxisStyle "Intensity"
     |> Chart.withSize (900., 900.)