diff options
Diffstat (limited to 'views/prediction.haml')
| -rw-r--r-- | views/prediction.haml | 127 |
1 files changed, 48 insertions, 79 deletions
diff --git a/views/prediction.haml b/views/prediction.haml index dfc11fc..91f7024 100644 --- a/views/prediction.haml +++ b/views/prediction.haml @@ -18,89 +18,58 @@ %tbody %tr %td{:id=>"compound", :style=>"vertical-align:top;"} - %a.btn.btn-link{:href => "#detailsTop", :id=>"linkCompound", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(@compound.uri)}/details")}} - %img.img-responsive{:src=>"#{@compound.uri}/image", :alt=>"no image", :title=>"#{@compound.smiles}", :width=>"150", :height=>"150"} - - count=0 - - @predictions.each do |pa| - / unpack to single array/prediction - / if p.data_entries array[0].size == 3 -> database hit - / change 'result' if database hit - / change 'confidence' if database hit - - pa.each do |p| - / prevent conversion of nil - /- $logger.debug "data entries in prediction array:\t#{p.data_entries}\n" - - database_hit = 0 - - if p.data_entries[0].size == 3 - - database_hit = 1 - - c = p.data_entries[0][0] != nil ? p.data_entries[0][0] : '' - - case c - - when /(false|true|inactive|active)/i - - c = c - - else - /- c = Array.new - - c = (p.data_entries[0][0].class == Float) ? p.data_entries[0][0].round(3) : (p.data_entries[0][0] != nil ? p.data_entries[0][0] : "no prediction") - %td{:style=>"vertical-align:top;"} - %b{:class => "title"} - = @prediction_models[count].title.gsub("_", " ") - - @model_uri = @prediction_models[count].uri + %a.btn.btn-link{:href => "#detailsTop", :id=>"linkCompound", data: { toggle: "modal", remote: to("/prediction/#{@compound.id.to_s}/details")}} + / %img.img-responsive{:src=>"#{@compound.id}/image", :alt=>"no image", :title=>"#{@compound.smiles}", :width=>"150", :height=>"150"} + = @compound.svg + - @predictions.each_with_index do |prediction,i| + %td{:style=>"vertical-align:top;"} + %b{:class => "title"} + = "#{@models[i].endpoint.gsub('_', ' ')} (#{@models[i].species})" + %p + - if prediction[:confidence] == "measured" + %p + / TODO fix scientific notation from database + %b Measured activity: + = prediction[:value].numeric? ? "#{prediction[:value].round(3)} (#{@models[i].unit})" : prediction[:value] + %p Compound is part of the training dataset + - elsif prediction[:neighbors].size > 0 %p / model type (classification|regression) %b Type: - = @model_type[count] + = @models[i].model.class.to_s.match("Classification") ? "Classification" : "Regression" + %br + %b Prediction: + / TODO scientific notation + = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} #{@models[i].unit}" : 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 <ul><li>a majority vote (weighted by compound similarity) for<br /><b>classification</b> (<a href='http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract', target='_blank'>original publication</a>) </li><li>a local QSAR model based on neighbors for<br /><b>regression</b> (<a href='http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract', target='_blank'</h>original publication</a>) </li></ul>Please keep in mind that predictions are based on the measured activities of neighbors."}} + %br + / TODO probability + %b Confidence: + = prediction[:confidence].round(3) + %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Confidence", data: {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."}} + %p + /TODO add tooltip for significant ftagments and descriptors + / - if @model_type[i] =~ /classification/i && (p.data_entries[0][1] != nil && p.data_entries[0][1] != 0.0) + / Significant fragments: + / %a.btn.btn-default.btn-sm{:id=>"linkSigFragments", :href => "#detailsTop", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(@model_uri)}/#{@model_type[i]}/#{CGI.escape(@compound.uri)}/fingerprints")}} Significant fragments + / - if @model_type[i] =~ /regression/i && (p.data_entries[0][1] != nil && p.data_entries[0][1] != 0.0) + / Descriptors + / %a.btn.btn-default.btn-sm{:id=>"linkDescriptors", :href => "#detailsTop", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(@model_uri)}/#{@model_type[i]}/#{CGI.escape(@compound.uri)}/fingerprints")}} Descriptors + / %p + %a.btn.btn-default.btn-sm{:href=> "#tabs", :id=>"link#{i+1}"} + Neighbors + :javascript + $("a#link#{i}").click(function () { + $(".results").show(); + //document.getElementById('tabs').focus(); + $('#neighborTabs a[href="#results_#{i+1}"]').tab('show'); + //$("#tabs").tabs({ active: "#{i}" }); + }); + %p + - else %p - - unless database_hit > 0 - %b Result: - %b - - if c.class == String - - result = (c != '' ? c : "No prediction result.") - = result - - else - - result = (c != '' ? c.round(3) : "No prediction result.") - = result - - confidence = (p.data_entries[0][1] != nil && p.data_entries[0][1] != 0.0) ? p.data_entries[0][1].round(2) : "--" - %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Result", 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 <ul><li>a majority vote (weighted by compound similarity) for<br /><b>classification</b> (<a href='http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract', target='_blank'>original publication</a>) </li><li>a local QSAR model based on neighbors for<br /><b>regression</b> (<a href='http://www.frontiersin.org/Journal/10.3389/fphar.2013.00038/abstract', target='_blank'</h>original publication</a>) </li></ul>Please keep in mind that predictions are based on the measured activities of neighbors."}} - - @cv = OpenTox::Validation.find @prediction_models[count].metadata[RDF::OT.crossValidation][0]+"/statistics" #unless @prediction_models[count].title.include?("Mutagenicity") - - unless @model_type[count] == "regression" - %br - %b - = "Probability: " - - unless result == "No prediction result." or confidence == "--" - - prob = @cv.probabilities( confidence, result )[:probs][result]*100 - = "#{prob.round(1)} %" - %p - %b Confidence: - = confidence - %a.btn.glyphicon.glyphicon-info-sign{:href=>"#", :title=>"Confidence", data: {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."}} - %p - /TODO add tooltip for significant ftagments and descriptors - - if @model_type[count] =~ /classification/i && (p.data_entries[0][1] != nil && p.data_entries[0][1] != 0.0) - / Significant fragments: - %a.btn.btn-default.btn-sm{:id=>"linkSigFragments", :href => "#detailsTop", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(@model_uri)}/#{@model_type[count]}/#{CGI.escape(@compound.uri)}/fingerprints")}} Significant fragments - - if @model_type[count] =~ /regression/i && (p.data_entries[0][1] != nil && p.data_entries[0][1] != 0.0) - / Descriptors - %a.btn.btn-default.btn-sm{:id=>"linkDescriptors", :href => "#detailsTop", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(@model_uri)}/#{@model_type[count]}/#{CGI.escape(@compound.uri)}/fingerprints")}} Descriptors - %p - - if c != '' - %a.btn.btn-default.btn-sm{:href=> "#tabs", :id=>"link#{count}"} - Neighbors - :javascript - $("a#link#{count}").click(function () { - $(".results").show(); - //document.getElementById('tabs').focus(); - $('#neighborTabs a[href="#results_#{count+1}"]').tab('show'); - //$("#tabs").tabs({ active: "#{count}" }); - }); - %p - - count+=1 - - else # database hit - %b Database hit: - %br Compound found in training dataset - %p - %b Measured activity: - = p.data_entries[0][2] - %p - - - count+=1 + Not enough similar compounds in training dataset. / always show the neighbors table, message is given there = haml :neighbors, :layout => false, :model_type => @model_type |