#1 : Add CP Heatmap Plot

CSBiology · Sep 4, 2020 · 1be3084 · 1be3084
1 parent 9fc3ed0
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Showing 6 changed files with 64 additions and 3 deletions.
diff --git a/README.md b/README.md
@@ -104,6 +104,15 @@ let SaRes =
 
     ![](./docs/img/cpTimeCourse.png)
 
+ - `TMEA.Plots.SurprisalAnalysis.plotPotentialHeatmap` is a more visually pleasing version of above plot (it omits the baseline state per default):
+
+    ```F#
+    SaRes
+    |> TMEA.Plots.SurprisalAnalysis.plotPotentialHeatmap true
+    ```
+
+    ![](./docs/img/cpHeatmap.png)
+
  - `Plots.SurprisalAnalysis.plotFreeEnergyLandscape` plots the free energy landscape of the given surprisal analysis result:
 
     ```

diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md
@@ -1,3 +1,6 @@
+#### 0.0.3-alpha - Friday, September 4, 2020 (WIP)
+- added Surprisal Analysis cp Heatmap Plot
+
 #### 0.0.2-alpha - Wednesday, September 2, 2020
 - added Plot functions for Surprisal Analysis results.
 - fixed Authors of the nuget package

diff --git a/TMEA.sln b/TMEA.sln
@@ -8,8 +8,10 @@ EndProject
 Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "Tools", "Tools", "{B543D949-2FB1-4745-9FBF-703B61558E8E}"
 	ProjectSection(SolutionItems) = preProject
 		build.fsx = build.fsx
+		.config\dotnet-tools.json = .config\dotnet-tools.json
 		fake.cmd = fake.cmd
 		fake.sh = fake.sh
+		global.json = global.json
 		paket.dependencies = paket.dependencies
 	EndProjectSection
 EndProject
@@ -20,6 +22,13 @@ Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "Github", "Github", "{30F2F4
 		README.md = README.md
 	EndProjectSection
 EndProject
+Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "Project", "Project", "{55D52760-ACF5-47D0-81DF-BEABF78443CC}"
+	ProjectSection(SolutionItems) = preProject
+		LICENSE = LICENSE
+		README.md = README.md
+		RELEASE_NOTES.md = RELEASE_NOTES.md
+	EndProjectSection
+EndProject
 Global
 	GlobalSection(SolutionConfigurationPlatforms) = preSolution
 		Debug|Any CPU = Debug|Any CPU

diff --git a/docs/img/cpHeatmap.png b/docs/img/cpHeatmap.png
diff --git a/src/TMEA/Playground.fsx b/src/TMEA/Playground.fsx
@@ -20,8 +20,6 @@ open FSharpAux
 #load "Frames.fs"
 #load "Plots.fs"
 
-
-
 open TMEA.IO
 open TMEA.SurprisalAnalysis
 open TMEA.MonteCarlo
@@ -152,6 +150,9 @@ open FSharp.Plotly
 SaRes
 |> TMEA.Plots.SurprisalAnalysis.plotConstraintTimecourses true
 
+SaRes
+|> TMEA.Plots.SurprisalAnalysis.plotPotentialHeatmap true
+
 SaRes
 |> TMEA.Plots.SurprisalAnalysis.plotFreeEnergyLandscape true data
 

diff --git a/src/TMEA/Plots.fs b/src/TMEA/Plots.fs
@@ -9,6 +9,12 @@ module Plots =
 
     module Presets =
 
+        let colorscale = StyleParam.Colorscale.Custom([
+            0.,"SteelBlue";
+            0.45,"LavenderBlush";
+            1.,"Salmon"
+        ])
+
         let standardConfig =
             Config.init (
                 Responsive = true,
@@ -80,7 +86,7 @@ module Plots =
                     |> Chart.withConfig Presets.standardConfig
                 else
                     c
-                    |> Chart.withX_AxisStyle "TP"
+                    |> Chart.withX_AxisStyle "TimePoint"
                     |> Chart.withY_AxisStyle "Free Energy / k<sub>b</sub>T"
                     |> Chart.withTitle "Free Energy Landscape"
 
@@ -89,3 +95,36 @@ module Plots =
             generateFreeEnergyLandscapePlot useStylePreset data saRes
             |> Chart.Show
 
+
+        let generatePotentialHeatmap (useStylePreset:bool) (saRes:SurprisalAnalysis.SAResult) =
+            saRes.Potentials
+               |> Matrix.toArray2D
+               |> JaggedArray.ofArray2D
+               |> Array.tail
+               |> Array.rev
+               |> JaggedArray.map (fun x -> x*10.)
+               |> fun potentials ->
+                    Chart.Heatmap(
+                        potentials,
+                        ColNames=[0 .. potentials.Length-1],
+                        RowNames = ([1..potentials.Length-1] |> List.map (sprintf "Constraint_%i") |> List.rev),
+                        Ygap=10,
+                        Colorscale= Presets.colorscale,zSmooth=StyleParam.SmoothAlg.Best
+                        )
+               |> Chart.withColorBar (Colorbar.init(Title="Constraint Potential"))
+               |> Chart.withTitle("PotentialTimeCourse")
+               |> fun c -> 
+                   if useStylePreset then
+                       c
+                       |> Presets.applyPresetStyle "Time point" "Constraint index" 
+                       |> Chart.withSize (1500.,1000.)
+                       |> Chart.withMargin (Margin.init(Left=100))
+                       |> Chart.withConfig Presets.standardConfig
+                   else
+                       c
+
+
+
+        let plotPotentialHeatmap (useStylePreset:bool) (saRes:SurprisalAnalysis.SAResult) =
+            generatePotentialHeatmap useStylePreset saRes
+            |> Chart.Show