diff options
Diffstat (limited to 'views')
| -rw-r--r-- | views/batch.haml | 106 | ||||
| -rw-r--r-- | views/details.haml | 8 | ||||
| -rw-r--r-- | views/faq_layout.haml | 67 | ||||
| -rw-r--r-- | views/layout.haml | 43 | ||||
| -rw-r--r-- | views/license.haml | 1 | ||||
| -rw-r--r-- | views/model_details.haml | 158 | ||||
| -rw-r--r-- | views/neighbors.haml | 24 | ||||
| -rw-r--r-- | views/predict.haml | 13 | ||||
| -rw-r--r-- | views/prediction.haml | 109 | ||||
| -rw-r--r-- | views/style.scss | 14 | ||||
| -rw-r--r-- | views/validation.haml | 16 |
11 files changed, 286 insertions, 273 deletions
diff --git a/views/batch.haml b/views/batch.haml index 9bfa67e..6c37a2b 100644 --- a/views/batch.haml +++ b/views/batch.haml @@ -2,57 +2,99 @@ %a.btn.btn-warning{:href => to('/predict')} %span.glyphicon.glyphicon-menu-left{:aria=>{:hidden=>"true"}} New Prediction - / displays all prediction result in first table + %a.btn.btn-success{:href=>"#{to("/predict/#{@filename}")}", :title=>"download"} + %span.glyphicon.glyphicon-download-alt + download CSV + + / show processed file name + %topline + %div.row + %div.col-md-4 + %h3 Batch Prediction Results: + %div.col-md-8 + %h3= @filename + + / displays all prediction result in one table %div.table-responsive %table.table.table-bordered{:id=>"batch", :style=>"background-color:white;"} - %thead - %tr - %h3.col-md-4{:style=>"padding-left:0;"} Batch Prediction Results: - %h3.col-md-8= @filename - %tr - %span.btn.btn-default - %a{:href=>"#{to("/predict/#{@filename}")}", :title=>"download"} - %span.glyphicon.glyphicon-download-alt{:aria=>{:hidden=>"true"}} - CSV %tbody - / key = compound, values = array of arrays with model, prediction + - if @warnings + - @warnings.each do |warning| + %tr + %td + %b Warning + %td + = warning.sub(/\b(tmp\/)\b/,"") + / key = compound, values = [model,prediction] - @batch.each do |key, values| - compound = key - - mw = compound.molecular_weight %tr %td{:style=>"vertical-align:top;"} %p= compound.svg %p= compound.smiles - / array = single prediction [endpoint, result] + + / array[0] = model, array[1] = prediction - values.each_with_index do |array,i| %td{:style=>"vertical-align:top;white-space:nowrap;"} - model = array[0] + / model type (classification|regression) + - model.model.class.to_s.match("Classification") ? type = "Classification" : type = "Regression" + - unit = model.unit - prediction = array[1] + %b{:class => "title"} = "#{model.endpoint.gsub('_', ' ')} (#{model.species})" - %p - - if prediction[:confidence] == "measured" + + / check for prediction + - if prediction[:neighbors].size > 0 %p - %b Measured activity: - - if prediction[:value].is_a?(Array) - = prediction[:value][0].numeric? ? prediction[:value].collect{|v| weight = compound.mmol_to_mg(v, mw); '%.2e' % v + " (#{model.unit})"+" | #{'%.2e' % weight} (mg/kg_bw/day)"}.join("</br>") : prediction[:value].join(", ") - - else - = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit}) | #{'%.2e' % compound.mmol_to_mg(prediction[:value], mw)} (mg/kg_bw/day)" : prediction[:value] + / show model type (classification|regression) + %b Type: + = type %p - %b Compound is part of the training dataset - - elsif prediction[:neighbors].size > 0 + / check for database hit + - if prediction[:warning] =~ /\b(identical)\b/i + + / show message about dbhit and measurements + %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] + + + / show prediction %p - / model type (classification|regression) - %b Type: - = model.model.class.to_s.match("Classification") ? "Classification" : "Regression" - %br - %b Prediction: - = 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: - = prediction[:confidence].round(3) + %b Prediction: + %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] + + / 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} - #{interval[0].delog10} (#{unit})" + %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? + %br + = "#{prediction[:probabilities].keys[0]}: #{prediction[:probabilities].values[0]}" + %br + / 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:"left", html:"true", content:"#{prediction[:warning]}"}} + + / no prediction - else %p = "Not enough similar compounds </br>in training dataset." diff --git a/views/details.haml b/views/details.haml index 8a57440..be4948a 100644 --- a/views/details.haml +++ b/views/details.haml @@ -1,8 +1,12 @@ +:javascript + $(document).ready(function(){ + addExternalLinks(); + }); %div.modal-body{:style=>"padding:10px;"} %button.close{ :type=>" button", data: { dismiss:"modal"}} × %h3 Names and synonyms: - %img.img-responsive{:src=>"#{@compound.uri}/image", :alt=>"Compound image not available", :width=>"300px", :heigth=>"300px", :style=>"float:left;"} + %p= @compound.svg %p %b="SMILES:" %p= @smiles @@ -19,6 +23,6 @@ %hr %p{:style=>"padding-left:0.5em;"} / pubchem link - %a.btn.btn-primary{:href=>"http://aop.in-silico.ch/", :title=>"Link opens in new window.", :alt=>"pubchem read across", :target=>"_blank"} PubChem read across + %a.btn.btn-primary{:href=>"http://aop.in-silico.ch/", :title=>"Link opens in new window.", :alt=>"pubchem read across", :rel=>"external"} PubChem read across %i (experimental) %br diff --git a/views/faq_layout.haml b/views/faq_layout.haml deleted file mode 100644 index a9b6664..0000000 --- a/views/faq_layout.haml +++ /dev/null @@ -1,67 +0,0 @@ -!!! -%html{:xmlns => "http://www.w3.org/1999/xhtml", "xml:lang" => "en", :lang => "en"} - %head - %meta{'charset'=>"utf-8"} - %meta{'http-equiv'=>"X-UA-Compatible", :content=>"IE=edge"} - %meta{'name'=>"viewport", :content=>"width=device-width, initial-scale=1"} - %title Lazar GUI FAQ - %link{:rel=>'icon', :type=>'image/x-icon', :href=>'/images/favicon.ico'} - %link{:rel=>'stylesheet', :href=>"#{'/css/bootstrap.min.css'}"} - %link{:rel=>'stylesheet', :href=>"#{'/css/theme.default.min.css'}"} - %link{:rel=>'stylesheet', :href=>"#{'/css/theme.bootstrap.min.css'}"} - %link{ :href=>"/style.css", :rel=>"stylesheet"} - %link{ :href=>"/stylesheets/jquery-ui.css", :rel=>"stylesheet"} - %script{:src=>"/javascripts/jquery-1.11.2.min.js"} - %script{:src=>"/javascripts/bootstrap.min.js"} - %script{ :src=>"/javascripts/lazar-gui.js"} - %body - %noscript - %div{ :style=>"width: 22em; position: absolute; left: 50%; margin-left: -11em; color: red; background-color: white; border: 1px solid red; padding: 4px; font-family: sans-serif"} - Your web browser must have JavaScript enabled in order for this application to display correctly. - %header.page-header - %div.row - %div.col-md-2 - %a{:href=> to("/predict")} - %img.media-object{:src=>"/images/ist_logo.png", :alt=>"logo", :style=>"margin:0 3em 0 2em;"} - %div.col-md-10 - %h1.media-heading{:style=>"margin: 0 0 0 1em;display:inline;"} Lazar GUI - A Graphical User Interface for the <a href="http://github.com/opentox/lazar">Lazar</a> framework - - %div.container-fluid - :javascript - $(document).ready(function(){ - $("#back-top").hide(); - $(".blind").error(function(){ - $(this).attr('src', '/images/blind.png'); - }); - }); - - = yield - - %footer.footer - %div.container-fluid - %p.text-muted - © - %a{:href => 'http://www.in-silico.ch', :rel => "external"} <i style="font-family: serife">in silico</i> toxicology gmbh 2004 - #{Time.now.year.to_s} - - #back-top{:style => "z-index:100;position:fixed;bottom:1%;right:1%;"} - %a{:href => "", :style=>"text:decoration:none;color:#ccc;"} - %span.glyphicon.glyphicon-circle-arrow-up{:style => "font-size:3em;color:black;"} - :javascript - $("#back-top").hide(); - $(function () { - $(window).scroll(function () { - if ($(this).scrollTop() > 600) { - $('#back-top').fadeIn(); - } else { - $('#back-top').fadeOut(); - } - }); - // scroll body to 0px on click - $('#back-top a').click(function () { - $('body,html').animate({ - scrollTop: 0 - }, 500); - return false; - }); - }); diff --git a/views/layout.haml b/views/layout.haml index 5d6d57a..8a920ea 100644 --- a/views/layout.haml +++ b/views/layout.haml @@ -15,7 +15,7 @@ %script{:src=>"/javascripts/bootstrap.min.js"} %script{:src=>"/javascripts/jquery.tablesorter.min.js"} %script{:src=>"/javascripts/jquery.tablesorter.widgets.js"} - %script{ :src=>"/javascripts/lazar-gui.js"} + %script{:src=>"/javascripts/lazar-gui.js"} %body %noscript %div{ :style=>"width: 22em; position: absolute; left: 50%; margin-left: -11em; color: red; background-color: white; border: 1px solid red; padding: 4px; font-family: sans-serif"} @@ -26,34 +26,35 @@ %a{:href=> to("/predict")} %img.media-object{:src=>"/images/IST_logo_s.png", :alt=>"logo", :width=>"150px", :heigth=>"150px", :style=>"margin:0 3em 0 2em;"} %div.col-md-8 - %h1.media-heading{:style=>"margin: 0 0 0 2em;"} + %h1.media-heading lazar toxicity predictions %div.col-md-2 %h1.media-heading %small - %a{:href=>"https://nano-lazar.in-silico.ch"} nano-lazar + %a{:href=>"https://nano-lazar.in-silico.ch", :rel=>"external"} nano-lazar %div.container-fluid %topline %div.row - %div.col-md-8 + %div.col-md-10 Problems, bugs, ideas for improvements ? Please report at our %a{:href => 'https://github.com/opentox/lazar-gui/issues', :rel => "external"} issue tracker - or send us an email - %a{ :href=>"mailto:info@in-silico.ch", :target=>"_top"} + , check out the + %a{:href=> to("/faq"), :rel => "external"} FAQ + page or send us an email. + %a{ :href=>"mailto:info@in-silico.ch?subject=[lazar v#{@version}]", :target=>"_top"} %img.share{:src=>"/images/Email.png"} - (version #{@version}). - %div.col-md-2 - %div.col-md-2 - %a{:href=>"https://twitter.com/intent/tweet?source=http%3A%2F%2Flazar.in-silico.ch&text=:%20http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Tweet"} + [version: #{@version}] + %div.col-md-2{:style=>"text-align:right;"} + %a{:href=>"https://twitter.com/intent/tweet?source=http%3A%2F%2Flazar.in-silico.ch&text=http%3A%2F%2Flazar.in-silico.ch", :rel=>"external", :title=>"Tweet"} %img.share{:src=>"/images/Twitter.png"} - %a{:href=>"https://plus.google.com/share?url=http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Share on Google+"} + %a{:href=>"https://plus.google.com/share?url=http%3A%2F%2Flazar.in-silico.ch", :rel=>"external", :title=>"Share on Google+"} %img.share{:src=>"/images/Google+.png"} - %a{:href=>"http://www.linkedin.com/shareArticle?mini=true&url=http%3A%2F%2Flazar.in-silico.ch&title=&summary=&source=http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Share on LinkedIn"} + %a{:href=>"http://www.linkedin.com/shareArticle?mini=true&url=http%3A%2F%2Flazar.in-silico.ch&title=&summary=&source=http%3A%2F%2Flazar.in-silico.ch", :rel=>"external", :title=>"Share on LinkedIn"} %img.share{:src=>"/images/LinkedIn.png"} - %a{:href=>"https://www.facebook.com/sharer/sharer.php?u=http%3A%2F%2Flazar.in-silico.ch&title=&summary=&source=http%3A%2F%2Flazar.in-silico.ch", :target=>"_blank", :title=>"Share on Facebook"} + %a{:href=>"https://www.facebook.com/sharer/sharer.php?u=http%3A%2F%2Flazar.in-silico.ch&title=&summary=&source=http%3A%2F%2Flazar.in-silico.ch", :rel=>"external", :title=>"Share on Facebook"} %img.share{:src=>"/images/Facebook.png"} - + :javascript $(document).ready(function(){ $("#back-top").hide(); @@ -77,17 +78,19 @@ %p.text-muted © %a{:href => 'http://www.in-silico.ch', :rel => "external"} <i style="font-family: serife">in silico</i> toxicology gmbh 2004 - #{Time.now.year.to_s} + | + %a{:href => to("/license"), :rel => "external"} GPL3 License %supporters.col-md-12 - %p Financial support: - %a{:href=>"http://www.bfr.bund.de/de/start.html", :target=>"_blank"} + %p Financial support by + %a{:href=>"http://www.bfr.bund.de/de/start.html", :rel=>"external"} %img{:src=>"/images/bfr_logo.gif"} - %a{:href=>"http://www.opentox.org/", :target=>"_blank"} + %a{:href=>"http://www.opentox.org/", :rel=>"external"} %img{:src=>"/images/ot_logo.png"} - %a{:href=>"https://enanomapper.net/", :target=>"_blank"} + %a{:href=>"https://enanomapper.net/", :rel=>"external"} %img{:src=>"/images/enm_logo.png"} - %a{:href=>"https://www.researchgate.net/institution/Nestle_SA/department/Nestle_Research_Center", :target=>"_blank"} + %a{:href=>"https://www.researchgate.net/institution/Nestle_SA/department/Nestle_Research_Center", :rel=>"external"} %img{:src=>"/images/nestec.jpg"} - + #back-top{:style => "z-index:100;position:fixed;bottom:1%;right:1%;"} %a{:href => "", :style=>"text:decoration:none;color:#ccc;"} diff --git a/views/license.haml b/views/license.haml new file mode 100644 index 0000000..2813220 --- /dev/null +++ b/views/license.haml @@ -0,0 +1 @@ += @license diff --git a/views/model_details.haml b/views/model_details.haml index 1be75e7..5c3aa4f 100644 --- a/views/model_details.haml +++ b/views/model_details.haml @@ -1,26 +1,43 @@ %b Model: %br Source: -%a{:href=>model.source, :target=>"external"} +%a{:href=>model.source, :rel=>"external"} = model.source %br - model.classification? ? type = "Classification" : type = "Regression" = "Type:\t" = type %br -- training_dataset = OpenTox::Dataset.find model.training_dataset.id +- training_dataset = OpenTox::Dataset.find model.model.training_dataset_id = "Training compounds:\t" -= training_dataset.compounds.size - += training_dataset.data_entries.size +%br += "Training dataset:\t" +%a{:href=>"#{to("/predict/dataset/#{training_dataset.name}")}"} + = training_dataset.name +%br +%b Algorithms: +%br +Similarity: +%a{:href=> "http://www.rubydoc.info/gems/lazar/OpenTox%2F#{model.model.algorithms["similarity"]["method"].sub("::", "%2F")}", :rel=>"external"} + = model.model.algorithms["similarity"]["method"] += ", min: #{model.model.algorithms["similarity"]["min"]}" +%br +Prediction: +%a{:href=>"http://www.rubydoc.info/gems/lazar/OpenTox%2F#{model.model.algorithms["prediction"]["method"].sub("::","%2f")}", :rel=>"external"} + = model.model.algorithms["prediction"]["method"] +%br +Descriptors: += model.model.algorithms["descriptors"]["method"]+"," += model.model.algorithms["descriptors"]["type"] %p - if type == "Classification" %b Independent crossvalidations: - else %b Independent crossvalidations (-log10 transformed): %div.row{:id=>"validations#{model.id}", :style=>"background-color:#f5f5f5;"} - - model.crossvalidations.each do |crossvalidation| + - crossvalidations.each do |cv| %span.col-xs-4.col-sm-4.col-md-4.col-lg-4 - - cv = OpenTox::CrossValidation.find crossvalidation.id = "Num folds:\t" = cv.folds %br @@ -34,76 +51,83 @@ Source: = "Accuracy:\t" = cv.accuracy.round(3) if cv.accuracy %br - = "True positive rate:\t" - = cv.true_rate["active"].round(3) if cv.true_rate["active"] - %br - = "True negative rate:\t" - = cv.true_rate["inactive"].round(3) if cv.true_rate["inactive"] - %br - = "Positive predictive value:\t" - = cv.predictivity["active"].round(3) if cv.predictivity["active"] - %br - = "Negative predictive value:\t" - = cv.predictivity["inactive"].round(3) if cv.predictivity["inactive"] + = "Weighted accuracy:\t" + = cv.weighted_accuracy.round(3) if cv.weighted_accuracy + - if cv.true_rate + %br + = "True positive rate:\t" + = cv.true_rate[cv.accept_values[0]].round(3) + %br + = "True negative rate:\t" + = cv.true_rate[cv.accept_values[1]].round(3) + - if cv.predictivity + %br + = "Positive predictive value:\t" + = cv.predictivity[cv.accept_values[0]].round(3) + %br + = "Negative predictive value:\t" + = cv.predictivity[cv.accept_values[1]].round(3) %p - %b Confusion Matrix: - %table.table.table-condensed.table-borderless{:style=>"width:20%;"} - %tbody - %tr - %td - %td - %td - %b actual - %td - %td - %tr - %td - %td - %td active - %td inactive - -#%td total - %tr - %td - %b predicted - %td active - %td - =cv.confusion_matrix[0][0] - %td - =cv.confusion_matrix[0][1] - -#%td - =cv.confusion_matrix[0][0]+cv.confusion_matrix[0][1] - %tr - %td - %td inactive - %td - =cv.confusion_matrix[1][0] - %td - =cv.confusion_matrix[1][1] - -#%td - =cv.confusion_matrix[1][0]+cv.confusion_matrix[1][1] - -#%tr - %td - %td total - %td - =cv.confusion_matrix[0][0]+cv.confusion_matrix[1][0] - %td - =cv.confusion_matrix[0][1]+cv.confusion_matrix[1][1] - %td - -#= "Confusion Matrix:\t" - -#= cv.confusion_matrix + - ["confusion_matrix", "weighted_confusion_matrix"].each_with_index do |matrix,idx| + %b= (idx == 0 ? "Confusion Matrix" : "Weighted Confusion Matrix") + %table.table.table-condensed.table-borderless{:style=>"width:20%;"} + %tbody + %tr + %td + %td + %td + %b actual + %td + %td + %tr + %td + %td + %td active + %td inactive + -#%td total + %tr + %td + %b predicted + %td active + %td + =( idx == 1 ? cv.send(matrix)[0][0].round(3) : cv.send(matrix)[0][0]) + %td + =( idx == 1 ? cv.send(matrix)[0][1].round(3) : cv.send(matrix)[0][1]) + -#%td + =cv.confusion_matrix[0][0]+cv.confusion_matrix[0][1] + %tr + %td + %td inactive + %td + =( idx == 1 ? cv.send(matrix)[1][0].round(3) : cv.send(matrix)[1][0]) + %td + =( idx == 1 ? cv.send(matrix)[1][1].round(3) : cv.send(matrix)[1][1]) + -#%td + =cv.confusion_matrix[1][0]+cv.confusion_matrix[1][1] + -#%tr + %td + %td total + %td + =cv.confusion_matrix[0][0]+cv.confusion_matrix[1][0] + %td + =cv.confusion_matrix[0][1]+cv.confusion_matrix[1][1] + %td + -#= "Confusion Matrix:\t" + -#= cv.confusion_matrix + %br %br /= "Confidence plot:" /%p.plot / %img{:src=>"confp#{cv.id}.svg"} - if model.regression? %br - = "Root mean squared error:\t" + %a.ht5{:href=>"https://en.wikipedia.org/wiki/Root-mean-square_deviation", :rel=>"external"} RMSE: = cv.rmse.round(3) if cv.rmse %br - = "Mean absolute error:\t" + %a.ht5{:href=>"https://en.wikipedia.org/wiki/Mean_absolute_error", :rel=>"external"} MAE: = cv.mae.round(3) if cv.mae %br - = "R square:\t" + %a.ht5{:href=>"https://en.wikipedia.org/wiki/Coefficient_of_determination", :rel=>"external"}= "R"+"<sup>2</sup>"+":" = cv.r_squared.round(3) if cv.r_squared %br /= "Confidence plot:" @@ -113,5 +137,5 @@ Source: /= "Correlation plot" /%p.plot / %img{:src=>"/corrp#{cv.id}.svg"} - -%br + +%br diff --git a/views/neighbors.haml b/views/neighbors.haml index 096e432..2d7c4a5 100644 --- a/views/neighbors.haml +++ b/views/neighbors.haml @@ -67,10 +67,10 @@ Compound %th.sorter-false{:style =>"vertical-align:middle;"} Measured Activity - %a.btn.glyphicon.glyphicon-info-sign{:href=>"#neighbors", :title=>"Measured Activity", :tabindex=>"0", data: {trigger:"focus", container:"body", toggle:"popover", placement:"left", html:"true", content:"Experimental result(s) from the training dataset."}, :style=>"z-index:auto+10;"} + %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"Measured Activity", :tabindex=>"0", data: {trigger:"focus", container:"body", toggle:"popover", placement:"auto", html:"true", content:"Experimental result(s) from the training dataset."}, :style=>"z-index:auto+10;"} %th.sorter-false{:style =>"vertical-align:middle;"} Similarity - %a.btn.glyphicon.glyphicon-info-sign{:href=>"#neighbors", :title=>"Similarity", :tabindex=>"0", data: {trigger:"focus", container:"body", toggle:"popover", placement:"left", html:"true", content:"<a href=\"https://en.wikipedia.org/wiki/Jaccard_index\">Tanimoto/Jaccard</a> similarity based on <a href=\"https://openbabel.org/docs/dev/FileFormats/MolPrint2D_format.html\">Molprint2D</a> fingerprints."}, :style=>"z-index:auto+10;"} + %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"Similarity", :tabindex=>"0", data: {trigger:"focus", container:"body", toggle:"popover", placement:"auto", html:"true", content:"<a alt=\"Link opens in new window.\" title=\"Link opens in new window.\" target=\"_blank\" href=\"https://en.wikipedia.org/wiki/Jaccard_index\">Tanimoto/Jaccard</a> similarity based on <a alt=\"Link opens in new window.\" title=\"Link opens in new window.\" target=\"_blank\" href=\"https://openbabel.org/docs/dev/FileFormats/MolPrint2D_format.html\">Molprint2D</a> fingerprints."}, :style=>"z-index:auto+10;"} / %th{:style =>"vertical-align:middle;"} / Supporting Information %tbody @@ -79,20 +79,22 @@ - prediction[:neighbors].uniq.each_with_index do |neighbor,count| %tr / Compound - - c = Compound.find(neighbor["_id"]) + - c = Compound.find(neighbor) %td{:style =>"vertical-align:middle;padding-left:1em;width:50%;"} - /%a.btn.btn-link{:href => "#details#{j+1}", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(neighbor["_id"])}/details"), :id=>"link#{j+1}#{count}"}} - %p= c.svg + %a.btn.btn-link{:href => "#details#{j+1}", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(c.id.to_s)}/details"), :id=>"link#{j+1}#{count}"}} + = c.svg %p= c.smiles - - mw = c.molecular_weight - / Measured Activity = compound.features + + / Measured Activity %td{:style =>"vertical-align:middle;padding-left:1em;width:20%;white-space:nowrap;"} - - features = c.features.collect{|k,v| v if k == predictionFeature[j]["id"] }.compact.flatten - = (predictionFeature[j]["type"] == "numeric") ? features.collect{|v| weight = c.mmol_to_mg(v); '%.2e' % v + " (#{@models[j].unit})"+" , #{'%.2e' % weight} #{(unit == "mmol/L") ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("</br>") : features.join("</br>") + - if neighbor[:measurement].is_a?(Array) + = (type == "Regression") ? neighbor[:measurement].collect{|value| "#{value.delog10.signif(3)} (#{unit})</br>#{c.mmol_to_mg(value.delog10).signif(3)} #{unit =~ /mmol\/L/ ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("</br>") : neighbor[:measurement].join(", ") + - else + = (type == "Regression") ? "#{neighbor[:measurement].delog10.signif(3)} (#{unit})</br>#{c.mmol_to_mg(neighbor[:measurement].delog10).signif(3)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : neighbor[:measurement] + / Similarity = tanimoto %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? - = neighbor[:tanimoto] != nil ? neighbor[:tanimoto].to_f.round(3) : "Not enough similar compounds </br>in training dataset." + = neighbor[:similarity].round(3) - else %span.btn.btn-default.disabled diff --git a/views/predict.haml b/views/predict.haml index 010ed12..59630d0 100644 --- a/views/predict.haml +++ b/views/predict.haml @@ -111,7 +111,7 @@ }; // whole site content needs to be in one form. Input and checkboxes are proofed by js functions. -%form{:name => "form", :action => to('/predict'), :method => "post", :enctype => "multipart/form-data", :onsubmit => "return !!(showcircle())" } +%form{:name => "form", :action => to('/predict'), :method => "post", :enctype => "multipart/form-data", :onsubmit => "return !!(showcircle())" } %fieldset#top.well %h2 1. Draw a chemical structure #insert @@ -125,11 +125,13 @@ %br %input{:type => 'text', :name => 'identifier', :id => 'identifier', :size => '60'} %p - %label{:for=>"fileselect"} + -#%label{:for=>"fileselect"} or upload a CSV file for batch predictions (disabled in public version) - %br - %span.btn.btn-default.btn-file - %input{:type=>"file", :name=> "fileselect", :id=>"fileselect", :accept=>"text/csv", :disabled=>"disabled"} + -#%a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"File format", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"auto", html:"true", content:"One column with compounds and keyword SMILES or InChI in the first row."}} + -#%br + -#%span.btn.btn-default.btn-file + -#%input{:type=>"file", :name=> "fileselect", :id=>"fileselect", :accept=>"text/csv", :disabled=>"disabled"} + %input{:type=>"hidden", :name=> "fileselect", :id=>"fileselect", :accept=>"text/csv", :disabled=>"disabled"} %fieldset#middle.well %h2 2. Select one or more endpoints @@ -162,6 +164,7 @@ document.getElementById("details#{model.id}").appendChild(details); $(button).show(); $(image).hide(); + addExternalLinks(); }); } } diff --git a/views/prediction.haml b/views/prediction.haml index 0f3d57b..1b8d38d 100644 --- a/views/prediction.haml +++ b/views/prediction.haml @@ -1,10 +1,3 @@ -:javascript - $(document).ready(function(){ - $('[data-toggle="popover"]').popover(); - $('.modal').on('hidden.bs.modal', function () { - $(this).removeData('bs.modal'); - }); - }); %div.well %a.btn.btn-warning{:href => to('/predict')} %i.glyphicon.glyphicon-menu-left @@ -16,9 +9,9 @@ %tbody %tr %td{:id=>"compound", :style=>"vertical-align:top;"} - %p= @compound.svg + %a.btn.btn-link{:href => "#details0", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(@compound.id.to_s)}/details"), :id=>"link01"}} + = @compound.svg %p= @compound.smiles - - mw = @compound.molecular_weight - @model_types = {} - @dbhit = {} - @predictions.each_with_index do |prediction,i| @@ -28,52 +21,66 @@ %td{:style=>"vertical-align:top;white-space:nowrap;"} %b{:class => "title"} = "#{@models[i].endpoint.gsub('_', ' ')} (#{@models[i].species})" - %p - - if prediction[:confidence] == "measured" - - @dbhit[i] = true + + / check for prediction + - if prediction[:neighbors].size > 0 %p - %b Measured activity: - - p prediction[:value] - - if prediction[:value].is_a?(Array) - = (type == "Regression") ? prediction[:value].collect{|v| weight = Compound.from_smiles(@compound.smiles).mmol_to_mg(v); '%.2e' % v + " (#{unit})"+", #{'%.2e' % weight} #{unit == "mmol/L" ? "(mg/L)" : "(mg/kg_bw/day)"}"}.join("</br>") : prediction[:value].join(", ") - - else - = (type == "Regression") ? "#{"%.2e" % prediction[:value]} (#{unit}), #{'%.2e' % @compound.mmol_to_mg(prediction[:value])} #{(unit == "mmol/L") ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value] - %p - %b Compound is part of the training dataset - - elsif prediction[:neighbors].size > 0 - %p - / model type (classification|regression) + / show model type (classification|regression) %b Type: = type - %br - %b Prediction: - = (type == "Regression") ? "#{'%.2e' % prediction[:value]} (#{unit}) , #{'%.2e' % @compound.mmol_to_mg(prediction[:value])} #{(unit == "mmol/L") ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:value] - / tabindex=0 seems the best fix for FF|S browsers on OSX better than trigger="click focus" which ends up in double click for FF. - / 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 - - if type == "Regression" - %b 95% Prediction interval: - - interval = prediction[:prediction_interval].nil? ? " - - " : prediction[:prediction_interval].collect{|i| i.round(2)} - %br - = "#{interval[0]} - #{interval[1]} (#{unit}), #{'%.2e' % @compound.mmol_to_mg(interval[0])} - #{'%.2e' % @compound.mmol_to_mg(interval[1])} #{(unit == "mmol/L") ? "(mg/L)" : "(mg/kg_bw/day)"}" - / prediction intervall 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."}} + %p + / check for database hit + - if prediction[:warning] =~ /\b(identical)\b/i + - @dbhit[i] = true + + / show message about dbhit and measurements + %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.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(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" : prediction[:measurements] + - else - %b Confidence: - = prediction[:confidence].round(2) unless prediction[:confidence].nil? - / confidence 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."}} + - @dbhit[i] = false + + / show prediction %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", :tabindex=>"0", 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", :tabindex=>"0", data: { toggle: "modal", remote: to("/prediction/#{CGI.escape(@model_uri)}/#{@model_type[i]}/#{CGI.escape(@compound.uri)}/fingerprints")}} Descriptors - / %p + %b Prediction: + / prediction popover + %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :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.signif(3)} (#{unit})</br>#{@compound.mmol_to_mg(prediction[:value].delog10).signif(3)} #{(unit =~ /\b(mol\/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]) + / prediction interval popover + %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :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.signif(3)} - #{interval[0].delog10.signif(3)} (#{unit})" + %br + = "#{@compound.mmol_to_mg(interval[1].delog10).signif(3)} - #{@compound.mmol_to_mg(interval[0].delog10).signif(3)} #{(unit =~ /\b(mol\/L)\b/) ? "(mg/L)" : "(mg/kg_bw/day)"}" if !prediction[:prediction_interval].nil? + - else + %b Probability: + / probability popover + %a.btn.glyphicon.glyphicon-info-sign{:href=>"javascript:void(0)", :title=>"Pobability", :tabindex=>"0", data: {trigger:"focus", toggle:"popover", placement:"left", html:"true", content:"Probability that the prediction belongs to one of the given classes."}} + - unless prediction[:probabilities].nil? + %br + = "#{prediction[:probabilities].keys[0]}: #{prediction[:probabilities].values[0].signif(3)}" + %br + = "#{prediction[:probabilities].keys[1]}: #{prediction[:probabilities].values[1].signif(3)}" + + / 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 @@ -81,4 +88,8 @@ / always show the neighbors table, message is given there = haml :neighbors, :layout => false, :model_type => @model_types, :dbhit => @dbhit + +%div.modal.fade{:id=>"details0", :role=>"dialog"} + %div.modal-dialog.modal-lg + %div.modal-content diff --git a/views/style.scss b/views/style.scss index 49e03ab..2c84781 100644 --- a/views/style.scss +++ b/views/style.scss @@ -51,10 +51,12 @@ ul.share-buttons{ padding: 0 2px 1px 2px !important; } .page-header{ - margin:20px 0 20px; - text-align:justify; + background-color: #fff; + padding:20px 0 20px 0; + margin: 0; + text-align:center; display:inline-block; - width:98.5%; + width:100%; } .share{ width: 30px; @@ -62,9 +64,13 @@ ul.share-buttons{ } supporters{ background-color: white; - + text-align:center; img{ width: 200px; margin-right: 1em; } } + +.footer{ + margin-top:3em; +} diff --git a/views/validation.haml b/views/validation.haml deleted file mode 100644 index fd63ea6..0000000 --- a/views/validation.haml +++ /dev/null @@ -1,16 +0,0 @@ -- case @model_type -- when "classification" - - prediction = @cv.metadata["http://www.opentox.org/api/1.2#classificationStatistics"]["http://www.opentox.org/api/1.2#numCorrect"] + @cv.metadata["http://www.opentox.org/api/1.2#classificationStatistics"]["http://www.opentox.org/api/1.2#numIncorrect"] - %p= "Number of predictions: #{prediction}" - - percent = @cv.metadata["http://www.opentox.org/api/1.2#classificationStatistics"]["http://www.opentox.org/api/1.2#percentCorrect"] - %p= "Correct predictions: #{percent.round(2)} %" -- when "regression" - - prediction = @cv.metadata["http://www.opentox.org/api/1.2#numInstances"].to_i - @cv.metadata["http://www.opentox.org/api/1.2#numUnpredicted"].to_i - %p= "Number of predictions: #{prediction}" - - rSquare = @cv.metadata["http://www.opentox.org/api/1.2#regressionStatistics"]["http://www.opentox.org/api/1.2#rSquare"] - %p= "R-squared: #{rSquare.round(2)} %" - - rootMeanSquaredError = @cv.metadata["http://www.opentox.org/api/1.2#regressionStatistics"]["http://www.opentox.org/api/1.2#rootMeanSquaredError"] - %p= "Root Mean Square Error: #{rootMeanSquaredError.round(2)} %" - - meanAbsoluteError = @cv.metadata["http://www.opentox.org/api/1.2#regressionStatistics"]["http://www.opentox.org/api/1.2#meanAbsoluteError"] - %p= "Mean Absolute Error: #{meanAbsoluteError.round(2)} %" - |