diff --git a/src/TMEA.Dash/TMEA.Dash.fsproj b/src/TMEA.Dash/TMEA.Dash.fsproj index 77734f1..bad22e9 100644 --- a/src/TMEA.Dash/TMEA.Dash.fsproj +++ b/src/TMEA.Dash/TMEA.Dash.fsproj @@ -26,7 +26,7 @@ - + diff --git a/src/TMEA/Frames.fs b/src/TMEA/Frames.fs index 86dc151..02f8eb9 100644 --- a/src/TMEA/Frames.fs +++ b/src/TMEA/Frames.fs @@ -4,13 +4,13 @@ module Frames = open Deedle - let private optDefFloat (f:float opt)= + let internal optDefFloat (f:float opt)= if f.HasValue then f.Value else -1. - let private optDefInt (f:int opt)= + let internal optDefInt (f:int opt)= if f.HasValue then f.Value else 0 - let createTMEACharacterizationTable minBinSize (termNameTransformation: string -> string) (tmeaCharacterizations:TMEACharacterization []) : Frame<(string*(string*int)),string> = + let internal createTMEACharacterizationTable minBinSize (termNameTransformation: string -> string) (tmeaCharacterizations:TMEACharacterization []) : Frame<(string*(string*int)),string> = tmeaCharacterizations |> Array.mapi (fun i desc -> let negFrame: Frame = @@ -105,16 +105,67 @@ module Frames = type TMEAResult with - static member toTMEACharacterizationFrame(tmeaRes:TMEAResult) = - tmeaRes.Characterizations |> createTMEACharacterizationTable 0 id - - static member toTMEACharacterizationFrame(minBinSize:int,tmeaRes:TMEAResult) = - tmeaRes.Characterizations |> createTMEACharacterizationTable minBinSize id + static member toTMEACharacterizationFrame(?MinBinSize:int, ?TermNameTransformation:string->string) = + + let minBinSize = defaultArg MinBinSize 0 + let termNameTransformation = defaultArg TermNameTransformation id + + fun (tmeaRes: TMEAResult) -> + tmeaRes.Characterizations |> createTMEACharacterizationTable minBinSize termNameTransformation - static member toTMEACharacterizationFrame (minBinSize:int,termNameTransformation:string->string,tmeaRes:TMEAResult) = - tmeaRes.Characterizations |> createTMEACharacterizationTable minBinSize termNameTransformation - static member toSignificanceMatrixFrame : unit = raise (System.NotImplementedException()) + static member toSignificanceMatrixFrame (?UseBenjaminiHochberg:bool, ?Threshold:float, ?TermNameTransformation:string->string) = + + let useBenjaminiHochberg = defaultArg UseBenjaminiHochberg false + let threshold = defaultArg Threshold 0.05 + let termNameTransformation = defaultArg TermNameTransformation id + + fun (tmeaRes:TMEAResult) -> + tmeaRes.Characterizations + |> Array.mapi (fun cI c -> + let pos = + c.PositiveDescriptor + |> Array.map (fun d -> + d.OntologyTerm => d.PValue + ) + + let neg = + c.PositiveDescriptor + |> Array.map (fun d -> + d.OntologyTerm => d.PValue + ) + + let keys, pos' = + if useBenjaminiHochberg then + neg + |> FSharp.Stats.Testing.MultipleTesting.benjaminiHochbergFDRBy id + |> Array.ofList + |> Array.unzip + else + neg + |> Array.unzip + + let keys, neg' = + if useBenjaminiHochberg then + neg + |> FSharp.Stats.Testing.MultipleTesting.benjaminiHochbergFDRBy id + |> Array.ofList + |> Array.unzip + else + neg + |> Array.unzip + + + $"C_{cI}" => ( + Array.map2 (fun p n -> if p < n then p else n) pos' neg' + |> Array.map (fun lowestPValue -> if lowestPValue < threshold then 1 else 0) + |> Array.zip keys + |> series + ) + ) + |> frame + |> Frame.fillMissingWith 0 + |> Frame.mapRowKeys (fun (name) -> (termNameTransformation name) => name) static member toConstraintsFrame : unit = raise (System.NotImplementedException()) diff --git a/src/TMEA/Playground.fsx b/src/TMEA/Playground.fsx index ba9b449..fbeee16 100644 --- a/src/TMEA/Playground.fsx +++ b/src/TMEA/Playground.fsx @@ -68,7 +68,7 @@ open Plotly.NET let characterizationFrame = testTmeaRes - |> TMEAResult.toTMEACharacterizationFrame + |> TMEAResult.toTMEACharacterizationFrame() characterizationFrame.Print() @@ -79,7 +79,7 @@ testTmeaRes |> TMEAResult.plotConstraintPotentialTimecourses(OmitBaselineState=true,InvertConstraints=[|1;2;3|], ConstraintCutoff=3) testTmeaRes -|> TMEAResult.plotPotentialHeatmap(ConstraintCutoff=3,InvertConstraints=[|2|]) +|> TMEAResult.plotConstraintPotentialHeatmap(ConstraintCutoff=3,InvertConstraints=[|2|]) testTmeaRes |> TMEAResult.plotFreeEnergyLandscape() @@ -94,6 +94,12 @@ testTmeaRes |> TMEAResult.plotFASWeightDistribution("signalling.light",[1;2;3],true,0.05) + +testTmeaRes +|> TMEAResult.toSignificanceMatrixFrame() +|> fun f -> f.Print() + + //readDataFrame // "TranscriptIdentifier" // "\t"