diff options
Diffstat (limited to 'views/prediction.haml')
| -rw-r--r-- | views/prediction.haml | 190 |
1 files changed, 123 insertions, 67 deletions
diff --git a/views/prediction.haml b/views/prediction.haml index b090be5..62bed8b 100644 --- a/views/prediction.haml +++ b/views/prediction.haml @@ -4,7 +4,14 @@ $('.modal').on('hidden.bs.modal', function () { $(this).removeData('bs.modal'); }); + /*TableExport.prototype.bootstrap = ["btn", "btn-default", "btn-toolbar"]; + var BootstrapTable = document.getElementById('overview'); + new TableExport(BootstrapTable, { + ignoreCSS: ".ignore", + bootstrap: true, + });*/ }); + %div.well %a.btn.btn-warning{:href => to('/predict')} %i.glyphicon.glyphicon-menu-left @@ -15,83 +22,132 @@ %table.table.table-bordered{:id=>"overview"} %tbody %tr - %td{:id=>"compound", :style=>"vertical-align:top;"} - %p= @compound.svg + %td{:id=>"compound"} + %b.title Compound + %p= embedded_svg @compound.svg, class: '.ignore', title: "#{@compound.smiles}" %p= @compound.smiles - @model_types = {} - @dbhit = {} - - @predictions.each_with_index do |prediction,i| - - type = @models[i].model.class.to_s.match("Classification") ? "Classification" : "Regression" - - @model_types[i] = type - - unit = @models[i].unit - %td{:style=>"vertical-align:top;white-space:nowrap;"} - %b{:class => "title"} - = "#{@models[i].endpoint.gsub('_', ' ')} (#{@models[i].species})" - - / check for prediction - - if prediction[:neighbors].size > 0 - %p - / show model type (classification|regression) - %b Type: - = type - %p - / check for database hit - - if prediction[:warning] =~ /\b(identical)\b/i - - @dbhit[i] = true - - / show message about dbhit and measurements + - toxtree = @predictions.pop if @toxtree == true + - unless @predictions.blank? + - @predictions.each_with_index do |prediction,i| + - if prediction.dimension > 0 + - sa_prediction = prediction[1] + - prediction = prediction[0] + - type = @models[i].model.class.to_s.match("Classification") ? "Classification" : "Regression" + - @model_types[i] = type + - unit = @models[i].unit + %td{:style=>"vertical-align:top;white-space:nowrap;"} + %b.title + = (sa_prediction ? "Consensus mutagenicity" : "#{@models[i].endpoint.gsub('_', ' ')} (#{@models[i].species})") + / check kazius + - if sa_prediction + - hash = sa_prediction[:prediction] + - confidence = sa_prediction[:confidence] + %p + %b Structural alerts: %p - %b Compound is part of the training dataset - %p - %b Measured activity: - %br - - if prediction[:measurements].is_a?(Array) - = (type == "Regression") ? prediction[:measurements].collect{|value| "#{value.delog10} (#{unit})</br>#{@compound.mmol_to_mg(value.delog10)} #{unit =~ /mmol\/L/ ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("</br>") : prediction[:measurements].join(", ") - - else - = (type == "Regression") ? "#{prediction[:measurements].delog10} (#{unit})</br>#{@compound.mmol_to_mg(prediction[:measurements].delog10)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:measurements] - - - else - - @dbhit[i] = false - - / show prediction - %p %b Prediction: - / prediction popover - -#%a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"<p>lazar searches the training dataset for similar compounds (neighbors) and calculates the prediction from their experimental activities.<p><b>Classification:</b></br>Majority vote of neighbor activities weighted by similarity.<p><b>Regression:</b></br>Prediction from a local partial least squares regression model with neighbor activities weighted by similarity.<p><a href=\"http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract\", target=\"_blank\"> Original publication</a>."}} %br - = (type == "Regression") ? "#{prediction[:value].delog10} (#{unit})</br>#{@compound.mmol_to_mg(prediction[:value].delog10)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value] + =(hash[:prediction] == true ? "mutagenic" : "non-mutagenic") + %p + %b Confidence: + %br + =confidence.to_f.signif(3) + %p + %b Structural alerts for mutagenicity: + %br + =hash[:matches].flatten.first + %p + / check for prediction + - if prediction[:neighbors] and !prediction[:value].nil? + %b.title= ("Lazar #{@models[i].endpoint.gsub('_', ' ').downcase} (#{@models[i].species}):" if sa_prediction) + %p + / show model type (classification|regression) + %b Type: + = type + %p + / check for database hit + - if prediction[:info] =~ /\b(identical)\b/i + - @dbhit[i] = true + / show message about dbhit and measurements + %p + :plain + This compound was part of the training dataset. <i>All</i> information </br> + from this compound was removed from the training data before the </br> + prediction, to obtain unbiased results. + %p + %b Measured activity: + %br + - if prediction[:measurements].is_a?(Array) + = (type == "Regression") ? prediction[:measurements].collect{|value| "#{value.delog10.signif(3)} (#{unit})</br>#{@compound.mmol_to_mg(value.delog10).signif(3)} #{unit =~ /mmol\/L/ ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("</br>") : prediction[:measurements].join(", ") + - else + = (type == "Regression") ? "#{prediction[:measurements].delog10.signif(3)} (#{unit})</br>#{@compound.mmol_to_mg(prediction[:measurements].delog10).signif(3)} #{(unit =~ /\b(mmol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:measurements] + + - else + - @dbhit[i] = false - / show prediction interval or probability + / show prediction %p - - if type == "Regression" - %b 95% Prediction interval: - - interval = (prediction[:prediction_interval].nil? ? nil : prediction[:prediction_interval]) - / prediction interval popover - -#%a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Prediction intervall", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"An estimate of prediction uncertainty. The \"real\" value should be with 95% probability within the prediction interval."}} - %br - = interval.nil? ? "--" : "#{interval[1].delog10} - #{interval[0].delog10} (#{unit})" + %b Prediction: %br - = "#{@compound.mmol_to_mg(interval[1].delog10)} - #{@compound.mmol_to_mg(interval[0].delog10)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" if !prediction[:prediction_interval].nil? - - else - %b Probability: - - unless prediction[:probabilities].nil? + = (type == "Regression") ? "#{prediction[:value].delog10.signif(3)} (#{unit})</br>#{@compound.mmol_to_mg(prediction[:value].delog10).signif(3)} #{(unit =~ /\b(mmol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value] + + / show prediction interval or probability + %p + - if type == "Regression" + %b 95% Prediction interval: + - interval = (prediction[:prediction_interval].nil? ? nil : prediction[:prediction_interval]) + %br + = interval.nil? ? "--" : "#{interval[1].delog10.signif(3)} - #{interval[0].delog10.signif(3)} (#{unit})" %br - = "#{prediction[:probabilities].keys[0]}: #{prediction[:probabilities].values[0]}" + = "#{@compound.mmol_to_mg(interval[1].delog10).signif(3)} - #{@compound.mmol_to_mg(interval[0].delog10).signif(3)} #{(unit =~ /\b(mmol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" if !interval.nil? + - else + %b Probability: + - unless prediction[:probabilities].nil? + %br + = "#{prediction[:probabilities].keys[0]}: #{prediction[:probabilities].values[0].signif(3)}" + - if prediction[:probabilities].size == 2 + %br + = "#{prediction[:probabilities].keys[1]}: #{prediction[:probabilities].values[1].signif(3)}" + + / show warnings and info + -#%p + - if !prediction[:info].blank? + %b Info: %br - = "#{prediction[:probabilities].keys[1]}: #{prediction[:probabilities].values[1]}" - / probability popover - -#%a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Confidence", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"Indicates the applicability domain of a model. Predictions with a high confidence can be expected to be more reliable than predictions with low confidence. Confidence values may take any value between 0 and 1. For most models confidence > 0.025 is a sensible (hard) cutoff to distinguish between reliable and unreliable predictions."}} - - / show warnings - %p - - if !prediction[:warning].nil? - %b Warnings: - %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"Warnings", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"auto", html:"true", content:"#{prediction[:warning]}"}} - - else - - @dbhit[i] = false - %p - = "Not enough similar compounds </br>in training dataset." + %p=prediction[:info].sub(/\'.*\'/,"").sub(/,/, ",<br>") + - if !prediction[:warnings].blank? + %b Warnings: + - prediction[:warnings].uniq.each do |warning| + %br + %p=warning.sub(/,/, ",<br>") + - else + %p + - if !prediction[:info].blank? + %b Info: + %br + %p=prediction[:info].sub(/\'.*\'/,"").sub(/,/, ",<br>") + - if !prediction[:warnings].blank? + %b Warnings: + - prediction[:warnings].uniq.each do |warning| + %p=warning.sub(/,/, ",<br>") + + / show Cramer rules if checked + - if @toxtree == true + %td{:style=>"vertical-align:top;white-space:nowrap;"} + %b.title Oral toxicity (Cramer rules) + %p + %b Cramer rules: + %br + =toxtree.first["Cramer rules"] + %p + %b Cramer rules, with extensions: + %br + =toxtree.last["Cramer rules, with extensions"] - / always show the neighbors table, message is given there - = haml :neighbors, :layout => false, :model_type => @model_types, :dbhit => @dbhit + / always show the neighbors table, message is given there. Except only Cramer is selected. + - unless @predictions.blank? + = haml :neighbors, :layout => false, :model_type => @model_types, :dbhit => @dbhit + |