diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/correlation/show_corr_results.py | 13 | ||||
| -rw-r--r-- | wqflask/wqflask/search_results.py | 18 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/show_trait.js | 36 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/collections/view.html | 36 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/correlation_page.html | 51 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/search_result_page.html | 55 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait_transform_and_filter.html | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/tool_buttons.html | 35 |
8 files changed, 103 insertions, 143 deletions
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 0c1cea0e..8536ce51 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -493,14 +493,15 @@ def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_ap results_dict['description'] = "N/A" results_dict['location'] = trait.location_repr results_dict['mean'] = "N/A" - results_dict['lrs_score'] = "N/A" results_dict['additive'] = "N/A" if bool(trait.description_display): results_dict['description'] = trait.description_display if bool(trait.mean): results_dict['mean'] = f"{float(trait.mean):.3f}" - if trait.LRS_score_repr != "N/A": - results_dict['lrs_score'] = f"{float(trait.LRS_score_repr):.1f}" + try: + trait_dict['lod_score'] = f"{float(this_trait.LRS_score_repr) / 4.61:.1f}" + except: + trait_dict['lod_score'] = "N/A" results_dict['lrs_location'] = trait.LRS_location_repr if bool(trait.additive): results_dict['additive'] = f"{float(trait.additive):.3f}" @@ -544,8 +545,10 @@ def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_ap else: results_dict['pubmed_link'] = trait.pubmed_link results_dict['pubmed_text'] = trait.pubmed_text - - results_dict['lrs_score'] = trait.LRS_score_repr + try: + trait_dict['lod_score'] = f"{float(this_trait.LRS_score_repr) / 4.61:.1f}" + except: + trait_dict['lod_score'] = "N/A" results_dict['lrs_location'] = trait.LRS_location_repr if bool(trait.additive): results_dict['additive'] = f"{float(trait.additive):.3f}" diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index ce836ce2..0d0894a4 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -126,11 +126,14 @@ views.py). trait_dict['mean'] = "N/A" trait_dict['additive'] = "N/A" if this_trait.mean != "" and this_trait.mean != None: - trait_dict['mean'] = '%.3f' % this_trait.mean - trait_dict['lrs_score'] = this_trait.LRS_score_repr + trait_dict['mean'] = f"{this_trait.mean:.3f}" + try: + trait_dict['lod_score'] = f"{float(this_trait.LRS_score_repr) / 4.61:.1f}" + except: + trait_dict['lod_score'] = "N/A" trait_dict['lrs_location'] = this_trait.LRS_location_repr if this_trait.additive != "": - trait_dict['additive'] = '%.3f' % this_trait.additive + trait_dict['additive'] = f"{this_trait.additive:.3f}" elif this_trait.dataset.type == "Geno": trait_dict['location'] = this_trait.location_repr elif this_trait.dataset.type == "Publish": @@ -143,12 +146,15 @@ views.py). trait_dict['pubmed_text'] = this_trait.pubmed_text trait_dict['mean'] = "N/A" if this_trait.mean != "" and this_trait.mean != None: - trait_dict['mean'] = '%.3f' % this_trait.mean - trait_dict['lrs_score'] = this_trait.LRS_score_repr + trait_dict['mean'] = f"{this_trait.mean:.3f}" + try: + trait_dict['lod_score'] = f"{float(this_trait.LRS_score_repr) / 4.61:.1f}" + except: + trait_dict['lod_score'] = "N/A" trait_dict['lrs_location'] = this_trait.LRS_location_repr trait_dict['additive'] = "N/A" if this_trait.additive != "": - trait_dict['additive'] = '%.3f' % this_trait.additive + trait_dict['additive'] = f"{this_trait.additive:.3f}" # Convert any bytes in dict to a normal utf-8 string for key in trait_dict.keys(): if isinstance(trait_dict[key], bytes): diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js index 87c35984..5dc9e456 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.js +++ b/wqflask/wqflask/static/new/javascript/show_trait.js @@ -731,14 +731,36 @@ filter_by_value = function() { } }; +hide_no_value_filter = function( settings, data, dataIndex ) { + this_value = table_api.column(3).nodes().to$()[dataIndex].childNodes[0].value; + if (this_value == "x"){ + return false + } else { + return true + } +} + hide_no_value = function() { - return $('.value_se').each((function(_this) { - return function(_index, element) { - if ($(element).find('.trait-value-input').val() === 'x') { - return $(element).hide(); + tables = ['samples_primary', 'samples_other']; + filter_active = $(this).data("active"); + for (_i = 0, _len = tables.length; _i < _len; _i++) { + table = tables[_i]; + if ($('#' + table).length) { + table_api = $('#' + table).DataTable(); + if (filter_active == "true"){ + $(this).val("Hide No Value") + table_api.draw(); + $(this).data("active", "false"); + } else { + $(this).val("Show No Value") + $.fn.dataTable.ext.search.push(hide_no_value_filter); + table_api.search(); + table_api.draw(); + $.fn.dataTable.ext.search.splice($.fn.dataTable.ext.search.indexOf(hide_no_value_filter, 1)); + $(this).data("active", "true"); } - }; - })(this)); + } + } }; $('#hide_no_value').click(hide_no_value); @@ -754,6 +776,7 @@ $('#block_outliers').click(block_outliers); reset_samples_table = function() { $('input[name="transform"]').val(""); $('span[name="transform_text"]').text("") + $('#hide_no_value').val("Hide No Value") tables = ['samples_primary', 'samples_other']; for (_i = 0, _len = tables.length; _i < _len; _i++) { table = tables[_i]; @@ -771,6 +794,7 @@ reset_samples_table = function() { this_node.value = this_node.attributes["data-value"].value; } } + table_api.draw(); } } }; diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html index 99a6f2de..66945ed7 100644 --- a/wqflask/wqflask/templates/collections/view.html +++ b/wqflask/wqflask/templates/collections/view.html @@ -28,41 +28,7 @@ {{ this_trait.name }}:{{ this_trait.dataset.name }}:{{ data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name)) }}, {% endfor %}" > - <button id="corr_matrix" class="btn btn-primary submit_special" data-url="/corr_matrix" title="Correlation Matrix" > - Correlations - </button> - - <button id="network_graph" class="btn btn-primary submit_special" data-url="/network_graph" title="Network Graph" > - Networks - </button> - - <button id="send_to_webgestalt" class="btn btn-primary submit_special" data-url="/webgestalt_page" title="WebGestalt" > - WebGestalt - </button> - - <button id="send_to_geneweaver" class="btn btn-primary submit_special" data-url="/geneweaver_page" title="GeneWeaver" > - GeneWeaver - </button> - - <button id="send_to_bnw" class="btn btn-primary submit_special" data-url="/bnw_page" title="Bayesian network software for causal modeling and reasoning, with an intuitive interface to incorporate biological knowledge and a complete pipeline from data to model to prediction" > - BNW - </button> - - <button id="wgcna_setup" class="btn btn-primary submit_special" data-url="/wgcna_setup" title="WGCNA Analysis" > - WGCNA - </button> - - <button id="ctl_setup" class="btn btn-primary submit_special" data-url="/ctl_setup" title="CTL Analysis" > - CTL Maps - </button> - - <button id="heatmap" class="btn btn-primary submit_special" data-url="/heatmap" title="Heatmap" > - MultiMap - </button> - - <button id="comp_bar_chart" class="btn btn-primary submit_special" data-url="/comparison_bar_chart" title="Comparison Bar Chart" > - Comparison Bar Chart - </button> + {% include 'tool_buttons.html' %} </form> </div> diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html index f6684ad7..8e2a23fd 100644 --- a/wqflask/wqflask/templates/correlation_page.html +++ b/wqflask/wqflask/templates/correlation_page.html @@ -32,42 +32,7 @@ {% for this_trait in trait_list %} {{ this_trait.name }}:{{ this_trait.dataset }}, {% endfor %}" > - - <button id="corr_matrix" class="btn btn-primary submit_special" data-url="/corr_matrix" title="Correlation Matrix" > - Correlations - </button> - - <button id="network_graph" class="btn btn-primary submit_special" data-url="/network_graph" title="Network Graph" > - Networks - </button> - - <button id="send_to_webgestalt" class="btn btn-primary submit_special" data-url="/webgestalt_page" title="WebGestalt" > - WebGestalt - </button> - - <button id="send_to_geneweaver" class="btn btn-primary submit_special" data-url="/geneweaver_page" title="GeneWeaver" > - GeneWeaver - </button> - - <button id="send_to_bnw" class="btn btn-primary submit_special" data-url="/bnw_page" title="Bayesian network software for causal modeling and reasoning, with an intuitive interface to incorporate biological knowledge and a complete pipeline from data to model to prediction" > - </button> - - <button id="wgcna_setup" class="btn btn-primary submit_special" data-url="/wgcna_setup" title="WGCNA Analysis" > - WGCNA - </button> - - <button id="ctl_setup" class="btn btn-primary submit_special" data-url="/ctl_setup" title="CTL Analysis" > - CTL Maps - </button> - - <button id="heatmap" class="btn btn-primary submit_special" data-url="/heatmap" title="Heatmap" > - MultiMap - </button> - - <button id="comp_bar_chart" class="btn btn-primary submit_special" data-url="/comparison_bar_chart" title="Comparison Bar Chart" > - Comparison Bar Chart - </button> - + {% include 'tool_buttons.html' %} </form> </div> <br /> @@ -119,14 +84,12 @@ <div class="show-hide-container" style="float: left; clear: left;"> <b>Show/Hide Columns:</b> <br> - <button class="toggle-vis" data-column="1">Index</button> - <button class="toggle-vis" data-column="2">Record</button> {% if target_dataset.type == 'ProbeSet' %} <button class="toggle-vis" data-column="3">Symbol</button> <button class="toggle-vis" data-column="4">Description</button> <button class="toggle-vis" data-column="5">Location</button> <button class="toggle-vis" data-column="6">Mean</button> - <button class="toggle-vis" data-column="7">High P</button> + <button class="toggle-vis" data-column="7">Peak LOD</button> <button class="toggle-vis" data-column="8">Peak Location</button> <button class="toggle-vis" data-column="9">Effect Size</button> {% elif target_dataset.type == 'Publish' %} @@ -137,7 +100,7 @@ <button class="toggle-vis" data-column="7">Sample {% if corr_method == 'pearson' %}r{% else %}rho{% endif %}</button> <button class="toggle-vis" data-column="8">N</button> <button class="toggle-vis" data-column="9">Sample p({% if corr_method == 'pearson' %}r{% else %}rho{% endif %})</button> - <button class="toggle-vis" data-column="10">High P</button> + <button class="toggle-vis" data-column="10">Peak LOD</button> <button class="toggle-vis" data-column="11">Peak Location</button> <button class="toggle-vis" data-column="12">Effect Size</button> {% else %} @@ -391,9 +354,9 @@ 'orderSequence': [ "desc", "asc"] }, { - 'title': "High P<a href=\"http://gn1.genenetwork.org/glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"> <i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a>", + 'title': "Peak <a href=\"{{ url_for('glossary_blueprint.glossary') }}#LRS\" target=\"_blank\" style=\"color: white;\"> <i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a>LOD", 'type': "natural-minus-na", - 'data': "lrs_score", + 'data': "lod_score", 'width': "60px", 'orderSequence': [ "desc", "asc"] }, @@ -491,9 +454,9 @@ 'orderSequence': [ "desc", "asc"] }, { - 'title': "High P<a href=\"http://gn1.genenetwork.org/glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"> <i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a>", + 'title': "Peak <a href=\"{{ url_for('glossary_blueprint.glossary') }}#LRS\" target=\"_blank\" style=\"color: white;\"> <i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a>LOD", 'type': "natural-minus-na", - 'data': "lrs_score", + 'data': "lod_score", 'width': "60px", 'orderSequence': [ "desc", "asc"] }, diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index 3be2e395..f2334512 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -75,42 +75,7 @@ {{ this_trait.name }}:{{ this_trait.dataset }}, {% endfor %}" > - - <button id="corr_matrix" class="btn btn-primary submit_special" data-url="/corr_matrix" title="Correlation Matrix" > - Correlations - </button> - - <button id="network_graph" class="btn btn-primary submit_special" data-url="/network_graph" title="Network Graph" > - Networks - </button> - - <button id="send_to_webgestalt" class="btn btn-primary submit_special" data-url="/webgestalt_page" title="WebGestalt" > - WebGestalt - </button> - - <button id="send_to_geneweaver" class="btn btn-primary submit_special" data-url="/geneweaver_page" title="GeneWeaver" > - GeneWeaver - </button> - - <button id="send_to_bnw" class="btn btn-primary submit_special" data-url="/bnw_page" title="Bayesian network software for causal modeling and reasoning, with an intuitive interface to incorporate biological knowledge and a complete pipeline from data to model to prediction" > - BNW - </button> - - <button id="wgcna_setup" class="btn btn-primary submit_special" data-url="/wgcna_setup" title="WGCNA Analysis" > - WGCNA - </button> - - <button id="ctl_setup" class="btn btn-primary submit_special" data-url="/ctl_setup" title="CTL Analysis" > - CTL Maps - </button> - - <button id="heatmap" class="btn btn-primary submit_special" data-url="/heatmap" title="Heatmap" > - MultiMap - </button> - - <button id="comp_bar_chart" class="btn btn-primary submit_special" data-url="/comparison_bar_chart" title="Comparison Bar Chart" > - Comparison Bar Chart - </button> + {% include 'tool_buttons.html' %} </form> </div> @@ -141,14 +106,12 @@ <div class="show-hide-container"> <b>Show/Hide Columns:</b> <br> - <button class="toggle-vis" data-column="1">Index</button> - <button class="toggle-vis" data-column="2">Record</button> {% if dataset.type == 'ProbeSet' %} <button class="toggle-vis" data-column="3">Symbol</button> <button class="toggle-vis" data-column="4">Description</button> <button class="toggle-vis" data-column="5">Location</button> <button class="toggle-vis" data-column="6">Mean</button> - <button class="toggle-vis" data-column="7">High P</button> + <button class="toggle-vis" data-column="7">Peak LOD</button> <button class="toggle-vis" data-column="8">Peak Location</button> <button class="toggle-vis" data-column="9">Effect Size</button> {% elif dataset.type == 'Publish' %} @@ -156,7 +119,7 @@ <button class="toggle-vis" data-column="4">Mean</button> <button class="toggle-vis" data-column="5">Authors</button> <button class="toggle-vis" data-column="6">Year</button> - <button class="toggle-vis" data-column="7">High P</button> + <button class="toggle-vis" data-column="7">Peak LOD</button> <button class="toggle-vis" data-column="8">Peak Location</button> <button class="toggle-vis" data-column="9">Effect Size</button> {% endif %} @@ -314,10 +277,10 @@ 'orderSequence': [ "desc", "asc"] }, { - 'title': "High P<a href=\"{{ url_for('glossary_blueprint.glossary') }}#LRS\" target=\"_blank\" style=\"color: white;\"> <i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a>", + 'title': "Peak <a href=\"{{ url_for('glossary_blueprint.glossary') }}#LRS\" target=\"_blank\" style=\"color: white;\"> <i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a>LOD", 'type': "natural-minus-na", - 'data': "lrs_score", - 'width': "65px", + 'data': "lod_score", + 'width': "60px", 'orderSequence': [ "desc", "asc"] }, { @@ -383,10 +346,10 @@ 'orderSequence': [ "desc", "asc"] }, { - 'title': "High P<a href=\"{{ url_for('glossary_blueprint.glossary') }}#LRS\" target=\"_blank\" style=\"color: white;\"> <i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a>", + 'title': "Peak <a href=\"{{ url_for('glossary_blueprint.glossary') }}#LRS\" target=\"_blank\" style=\"color: white;\"> <i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a>LOD", 'type': "natural-minus-na", - 'data': "lrs_score", - 'width': "80px", + 'data': "lod_score", + 'width': "60px", 'orderSequence': [ "desc", "asc"] }, { diff --git a/wqflask/wqflask/templates/show_trait_transform_and_filter.html b/wqflask/wqflask/templates/show_trait_transform_and_filter.html index d7eac378..b70ca590 100644 --- a/wqflask/wqflask/templates/show_trait_transform_and_filter.html +++ b/wqflask/wqflask/templates/show_trait_transform_and_filter.html @@ -80,7 +80,7 @@ <input type="button" id="filter_by_value" class="btn btn-danger" value="Filter"> </div> <div> - <input type="button" id="hide_no_value" class="btn btn-default" value="Hide No Value"> + <input data-active="false" type="button" id="hide_no_value" class="btn btn-default" value="Hide No Value"> <input type="button" id="block_outliers" class="btn btn-default" value="Block Outliers"> <input type="button" class="btn btn-success reset" value="Reset"> <span class="input-append"> diff --git a/wqflask/wqflask/templates/tool_buttons.html b/wqflask/wqflask/templates/tool_buttons.html new file mode 100644 index 00000000..5b2dbf3d --- /dev/null +++ b/wqflask/wqflask/templates/tool_buttons.html @@ -0,0 +1,35 @@ +<button id="corr_matrix" class="btn btn-primary submit_special" data-url="/corr_matrix" title="Correlation Matrix" > + Correlations +</button> + +<button id="network_graph" class="btn btn-primary submit_special" data-url="/network_graph" title="Network Graph" > + Networks +</button> + +<button id="send_to_webgestalt" class="btn btn-primary submit_special" data-url="/webgestalt_page" title="WebGestalt" > + WebGestalt +</button> + +<button id="send_to_geneweaver" class="btn btn-primary submit_special" data-url="/geneweaver_page" title="GeneWeaver" > + GeneWeaver +</button> + +<button id="send_to_bnw" class="btn btn-primary submit_special" data-url="/bnw_page" title="Bayesian network software for causal modeling and reasoning, with an intuitive interface to incorporate biological knowledge and a complete pipeline from data to model to prediction" > + BNW +</button> + +<button id="wgcna_setup" class="btn btn-primary submit_special" data-url="/wgcna_setup" title="WGCNA Analysis" > + WGCNA +</button> + +<button id="ctl_setup" class="btn btn-primary submit_special" data-url="/ctl_setup" title="CTL Analysis" > + CTL Maps +</button> + +<button id="heatmap" class="btn btn-primary submit_special" data-url="/heatmap" title="Heatmap" > + MultiMap +</button> + +<button id="comp_bar_chart" class="btn btn-primary submit_special" data-url="/comparison_bar_chart" title="Comparison Bar Chart" > + Comparison Bar Chart +</button> \ No newline at end of file |