From efd241beab11fbfc200f0c32ffb9e198ed406c83 Mon Sep 17 00:00:00 2001 From: gebele Date: Thu, 29 Oct 2015 18:20:39 +0000 Subject: added mg/kg_bw/day --- application.rb | 6 ++++-- views/batch.haml | 5 +++-- views/neighbors.haml | 6 ++++-- views/prediction.haml | 6 +++--- 4 files changed, 14 insertions(+), 9 deletions(-) diff --git a/application.rb b/application.rb index 229f3a1..1763e3a 100644 --- a/application.rb +++ b/application.rb @@ -202,14 +202,16 @@ get '/predict/?:csv?' do model = array[0] prediction = array[1] compound = key.smiles + mw = key.molecular_weight + weight = Compound.from_smiles(compound).mmol_to_mg(prediction[:value], mw) endpoint = "#{model.endpoint.gsub('_', ' ')} (#{model.species})" if prediction[:confidence] == "measured" type = "" - pred = prediction[:value].numeric? ? "#{prediction[:value].round(3)} (#{model.unit})" : prediction[:value] + pred = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit}) | #{'%.2e' % weight} (mg/kg_bw/day)" : prediction[:value] confidence = "measured activity" elsif prediction[:neighbors].size > 0 type = model.model.class.to_s.match("Classification") ? "Classification" : "Regression" - pred = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} #{model.unit}" : prediction[:value] + pred = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} #{model.unit} | #{'%.2e' % weight} (mg/kg_bw/day)" : prediction[:value] confidence = prediction[:confidence] else type = "" diff --git a/views/batch.haml b/views/batch.haml index ec987c4..f593188 100644 --- a/views/batch.haml +++ b/views/batch.haml @@ -18,6 +18,7 @@ / key = compound, values = array of arrays with model, prediction - @batch.each do |key, values| - compound = key + - mw = compound.molecular_weight %tr %td{:style=>"vertical-align:top;"} %p= compound.svg @@ -34,7 +35,7 @@ %p / TODO fix scientific notation from database %b Measured activity: - = prediction[:value].numeric? ? "#{prediction[:value].round(3)} (#{model.unit})" : prediction[:value] + = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit}) | #{'%.2e' % compound.mmol_to_mg(prediction[:value], mw)} (mg/kg_bw/day)" : prediction[:value] %p Compound is part of the training dataset - elsif prediction[:neighbors].size > 0 %p @@ -44,7 +45,7 @@ %br %b Prediction: / TODO scientific notation - = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit})" : prediction[:value] + = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit}) | #{'%.2e' % compound.mmol_to_mg(prediction[:value], mw)} (mg/kg_bw/day)" : prediction[:value] %br / TODO probability %b Confidence: diff --git a/views/neighbors.haml b/views/neighbors.haml index a741b45..4a1f3ea 100644 --- a/views/neighbors.haml +++ b/views/neighbors.haml @@ -65,9 +65,11 @@ /%a.btn.btn-link{:href => "#details#{j+1}", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(neighbor[0].to_s)}/details"), :id=>"link#{j+1}#{count}"}} %p= Compound.find(neighbor[0]).svg %p= Compound.find(neighbor[0]).smiles + - c = Compound.find(neighbor[0]) + - mw = c.molecular_weight / Measured Activity - %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;"} - = (type == "Regression") ? neighbor[2].collect{|n| '%.2e' % n + " (#{@models[j].unit})"}.join("
") : neighbor[2].join(", ") + %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;white-space:nowrap;"} + = (type == "Regression") ? neighbor[2].collect{|n| weight = c.mmol_to_mg(n, mw); '%.2e' % n + " (#{@models[j].unit})"+"|#{'%.2e' % weight} (mg/kg_bw/day)"}.join("
") : neighbor[2].join(", ") / Similarity %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;"} / TODO differentiate between no neighbors found and compound found in dataset, display neighbors for compounds in dataset? diff --git a/views/prediction.haml b/views/prediction.haml index ef0c5db..11d542e 100644 --- a/views/prediction.haml +++ b/views/prediction.haml @@ -18,6 +18,7 @@ %td{:id=>"compound", :style=>"vertical-align:top;"} %p= @compound.svg %p= @compound.smiles + - mw = @compound.molecular_weight - @model_types = {} - @dbhit = {} - @predictions.each_with_index do |prediction,i| @@ -32,7 +33,7 @@ %p / TODO fix scientific notation from database %b Measured activity: - = (type == "Regression") ? "#{"%.2e" % prediction[:value]} (#{@models[i].unit})" : prediction[:value] + = (type == "Regression") ? "#{"%.2e" % prediction[:value]} (#{@models[i].unit}) | #{'%.2e' % @compound.mmol_to_mg(prediction[:value], mw)} (mg/kg_bw/day)" : prediction[:value] %p Compound is part of the training dataset - elsif prediction[:neighbors].size > 0 %p @@ -41,8 +42,7 @@ = type %br %b Prediction: - / TODO scientific notation - = (type == "Regression") ? "#{'%.2e' % prediction[:value]} (#{@models[i].unit})" : prediction[:value] + = (type == "Regression") ? "#{'%.2e' % prediction[:value]} (#{@models[i].unit}) | #{'%.2e' % @compound.mmol_to_mg(prediction[:value], mw)} (mg/kg_bw/day)" : prediction[:value] / TODO update description / %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction", data: {toggle:"popover", placement:"left", html:"true", content:"LAZAR calculates searches the training dataset for similar compounds (neighbors) and calculates the prediction from their measured activities. LAZAR calculates predictions using Please keep in mind that predictions are based on the measured activities of neighbors."}} %br -- cgit v1.2.3