diff options
18 files changed, 323 insertions, 147 deletions
diff --git a/bin/genenetwork2 b/bin/genenetwork2 index 10e99d8b..21f0db13 100755 --- a/bin/genenetwork2 +++ b/bin/genenetwork2 @@ -25,7 +25,7 @@ # webserver) run from the base-dir with settings file and add that # script with a -c switch, e.g. # -# env GN2_PROFILE=/usr/local/guix-profiles/gn2-latest SQL_URI=mysql://webqtlout:webqtlout@lily.uthsc.edu/db_webqtl ./bin/genenetwork2 ./etc/default_settings.py -c ./maintenance/gen_select_dataset.py +# env GN2_PROFILE=/usr/local/guix-profiles/gn-latest-20181119 TMPDIR=/export/local/home/zas1024/gn2-zach/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5002 GENENETWORK_FILES=/export/local/home/zas1024/gn2-zach/genotype_files SQL_URI=mysql://webqtlout:webqtlout@lily.uthsc.edu/db_webqtl ./bin/genenetwork2 ./etc/default_settings.py -c ./maintenance/gen_select_dataset.py # # To run any script in the environment # diff --git a/wqflask/maintenance/generate_kinship_from_bimbam.py b/wqflask/maintenance/generate_kinship_from_bimbam.py index ad0eb036..b53f5dda 100644 --- a/wqflask/maintenance/generate_kinship_from_bimbam.py +++ b/wqflask/maintenance/generate_kinship_from_bimbam.py @@ -54,8 +54,8 @@ class GenerateKinshipMatrices(object): if __name__=="__main__": - Geno_Directory = """/home/zas1024/genotype_files/genotype/""" - Bimbam_Directory = """/home/zas1024/genotype_files/genotype/bimbam/""" + Geno_Directory = """/export/local/home/zas1024/genotype_files/genotype/""" + Bimbam_Directory = """/export/local/home/zas1024/genotype_files/genotype/bimbam/""" GenerateKinshipMatrices.process_all(Geno_Directory, Bimbam_Directory) #./gemma -g /home/zas1024/genotype_files/genotype/bimbam/BXD_geno.txt -p /home/zas1024/genotype_files/genotype/bimbam/BXD_pheno.txt -gk 1 -o BXD \ No newline at end of file diff --git a/wqflask/maintenance/geno_to_json.py b/wqflask/maintenance/geno_to_json.py index 789a1691..9579812a 100644 --- a/wqflask/maintenance/geno_to_json.py +++ b/wqflask/maintenance/geno_to_json.py @@ -24,6 +24,8 @@ import simplejson as json from pprint import pformat as pf +#from utility.tools import flat_files + class EmptyConfigurations(Exception): pass @@ -183,8 +185,8 @@ class ConvertGenoFile(object): if __name__=="__main__": - Old_Geno_Directory = """/home/zas1024/genotype_files/genotype/""" - New_Geno_Directory = """/home/zas1024/genotype_files/genotype/json/""" + Old_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype""" + New_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype/json""" #Input_File = """/home/zas1024/gene/genotype_files/genotypes/BXD.geno""" #Output_File = """/home/zas1024/gene/wqflask/wqflask/pylmm/data/bxd.snps""" #convertob = ConvertGenoFile("/home/zas1024/gene/genotype_files/genotypes/SRxSHRSPF2.geno", "/home/zas1024/gene/genotype_files/new_genotypes/SRxSHRSPF2.json") diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py index 31d47ff2..6d9f07a0 100644 --- a/wqflask/wqflask/show_trait/SampleList.py +++ b/wqflask/wqflask/show_trait/SampleList.py @@ -63,10 +63,7 @@ class SampleList(object): sample.extra_info['url'] = "/mouseCross.html#AXB/BXA" sample.extra_info['css_class'] = "fs12" - if sample_group_type == 'primary': - sample.this_id = "Primary_" + str(counter) - else: - sample.this_id = "Other_" + str(counter) + sample.this_id = str(counter) #### For extra attribute columns; currently only used by several datasets - Zach if self.sample_attribute_values: diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 34447853..7d6dd74e 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -153,7 +153,8 @@ class ShowTrait(object): hddn['group'] = self.temp_group hddn['species'] = self.temp_species hddn['use_outliers'] = False - hddn['method'] = "pylmm" + hddn['method'] = "gemma" + hddn['selected_chr'] = -1 hddn['mapping_display_all'] = True hddn['suggestive'] = 0 hddn['num_perm'] = 0 @@ -182,6 +183,11 @@ class ShowTrait(object): self.sample_group_types['samples_primary'] = self.dataset.group.name sample_lists = [group.sample_list for group in self.sample_groups] + #ZS: Get list of chromosomes to select for mapping + self.chr_list = [["All", -1]] + for i, this_chr in enumerate(self.species.chromosomes.chromosomes): + self.chr_list.append([self.species.chromosomes.chromosomes[this_chr].name, i]) + self.genofiles = get_genofiles(self.dataset) self.has_num_cases = has_num_cases(self.this_trait) diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css index aa47d13f..c03b6103 100644 --- a/wqflask/wqflask/static/new/css/show_trait.css +++ b/wqflask/wqflask/static/new/css/show_trait.css @@ -27,6 +27,10 @@ table.dataTable thead .sorting_desc { background-image: url("../packages/DataTables/images/sort_desc_disabled.png"); } +table.dataTable thead th { + padding: 4px 18px 4px 10px; +} + table.dataTable tbody td { padding: 3px 20px 1px 10px; } diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json index 9c806a7f..72008225 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json +++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json @@ -1557,6 +1557,42 @@ ] ] }, + "AIL-LGSM-F34-A": { + "Phenotypes": [ + [ + "None", + "AIL-LGSM-F34-APublish", + "AIL-LGSM-F34-A Phenotypes" + ] + ] + }, + "AIL-LGSM-F34-F39-43-GBS": { + "Phenotypes": [ + [ + "None", + "AIL-LGSM-F34-F39-43-GBSPublish", + "AIL-LGSM-F34-F39-43-GBS Phenotypes" + ] + ] + }, + "AIL-LGSM-F34-GBS": { + "Phenotypes": [ + [ + "None", + "AIL-LGSM-F34-GBSPublish", + "AIL-LGSM-F34-GBS Phenotypes" + ] + ] + }, + "AIL-LGSM-F39-43-GBS": { + "Phenotypes": [ + [ + "None", + "AIL-LGSM-F39-43-GBSPublish", + "AIL-LGSM-F39-43-GBS Phenotypes" + ] + ] + }, "AKXD": { "Genotypes": [ [ @@ -2591,6 +2627,11 @@ ], "Liver mRNA": [ [ + "857", + "EPFLMouseLiverCDHFDRMA0818", + "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA" + ], + [ "859", "EPFLMouseLiverCDRMA0818", "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA" @@ -2621,11 +2662,6 @@ "NIA Aging BXD HFD Liver Affy Clariom S Gene Level (Aug18) RMA **" ], [ - "857", - "EPFLMouseLiverCDHFDRMA0818", - "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA" - ], - [ "430", "EPFLMouseLiverRMA0413", "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA" @@ -2641,6 +2677,11 @@ "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA" ], [ + "848", + "EPFLMouseLiverHFCEx0413", + "EPFL/LISP BXD HFC Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level" + ], + [ "433", "EPFLMouseLiverBothExRMA0413", "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level" @@ -2651,11 +2692,6 @@ "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level" ], [ - "848", - "EPFLMouseLiverHFCEx0413", - "EPFL/LISP BXD HFC Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level" - ], - [ "700", "UTHSC-VGX_MmBXDHepatocytesRMA1014", "UT-VGX Hepatocytes Affy Mouse Gene 1.0 ST Gene Level (Oct14) RMA" @@ -4002,6 +4038,22 @@ "AIL Advanced Intercross Line" ], [ + "AIL-LGSM-F34-A", + "AIL LGSM F34 (Array)" + ], + [ + "AIL-LGSM-F34-GBS", + "AIL LGSM F34 (GBS)" + ], + [ + "AIL-LGSM-F34-F39-43-GBS", + "AIL LGSM F34 and F39-43 (GBS)" + ], + [ + "AIL-LGSM-F39-43-GBS", + "AIL LGSM F39-43 (GBS)" + ], + [ "AKXD", "AKXD RI Family" ], @@ -4929,6 +4981,30 @@ "Striatum mRNA" ] ], + "AIL-LGSM-F34-A": [ + [ + "Phenotypes", + "Phenotypes" + ] + ], + "AIL-LGSM-F34-F39-43-GBS": [ + [ + "Phenotypes", + "Phenotypes" + ] + ], + "AIL-LGSM-F34-GBS": [ + [ + "Phenotypes", + "Phenotypes" + ] + ], + "AIL-LGSM-F39-43-GBS": [ + [ + "Phenotypes", + "Phenotypes" + ] + ], "AKXD": [ [ "Genotypes", diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js index df86e764..717d98b9 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.js +++ b/wqflask/wqflask/static/new/javascript/show_trait.js @@ -417,16 +417,27 @@ } console.log("towards end:", sample_sets); update_stat_values(sample_sets); - console.log("redrawing histogram"); - redraw_histogram(); - console.log("redrawing bar chart"); - redraw_bar_chart(); - console.log("redrawing box plot"); - redraw_box_plot(); - console.log("redrawing violin plot"); - redraw_violin_plot(); - console.log("redrawing probability plot"); - return redraw_prob_plot(); + + if ($('#histogram').hasClass('js-plotly-plot')){ + console.log("redrawing histogram"); + redraw_histogram(); + } + if ($('#bar_chart').hasClass('js-plotly-plot')){ + console.log("redrawing bar chart"); + redraw_bar_chart(); + } + if ($('#box_plot').hasClass('js-plotly-plot')){ + console.log("redrawing box plot"); + redraw_box_plot(); + } + if ($('#violin_plot').hasClass('js-plotly-plot')){ + console.log("redrawing violin plot"); + redraw_violin_plot(); + } + if ($('#prob_plot_div').hasClass('js-plotly-plot')){ + console.log("redrawing probability plot"); + return redraw_prob_plot(); + } }; show_hide_outliers = function() { var label; @@ -853,7 +864,13 @@ } }; root.bar_layout = layout - Plotly.newPlot('bar_chart', root.bar_data, root.bar_layout, root.modebar_options) + $('.bar_chart_tab').click(function() { + if ($('#bar_chart').hasClass('js-plotly-plot')){ + redraw_bar_chart(); + } else { + Plotly.newPlot('bar_chart', root.bar_data, root.bar_layout, root.modebar_options) + } + }); } if (full_sample_lists.length > 1) { @@ -957,11 +974,18 @@ ] } - obj = { + box_obj = { data: box_data, layout: root.box_layout } - Plotly.newPlot('box_plot', obj, root.modebar_options); + + $('.box_plot_tab').click(function() { + if ($('#box_plot').hasClass('js-plotly-plot')){ + redraw_box_plot(); + } else { + Plotly.newPlot('box_plot', box_obj, root.modebar_options); + } + }); // Violin Plot @@ -1066,12 +1090,18 @@ ] } - obj = { + violin_obj = { data: violin_data, layout: root.violin_layout } - Plotly.plot('violin_plot', obj, root.modebar_options) + $('.violin_plot_tab').click(function() { + if ($('#violin_plot').hasClass('js-plotly-plot')){ + redraw_violin_plot(); + } else { + Plotly.plot('violin_plot', violin_obj, root.modebar_options); + } + }); // Histogram var hist_trace = { @@ -1091,9 +1121,16 @@ b: 60 } }; - Plotly.newPlot('histogram', data, layout, root.modebar_options) - update_histogram_width() + $('.histogram_tab').click(function() { + if ($('#histogram').hasClass('js-plotly-plot')){ + redraw_histogram(); + update_histogram_width(); + } else { + Plotly.newPlot('histogram', data, layout, root.modebar_options) + update_histogram_width() + } + }); $('.histogram_samples_group').val(root.stats_group); $('.histogram_samples_group').change(function() { @@ -1119,13 +1156,18 @@ root.prob_plot_group = 'samples_primary'; $('.prob_plot_samples_group').val(root.prob_plot_group); + $('.prob_plot_tab').click(function() { + return redraw_prob_plot(); + }); $('.prob_plot_samples_group').change(function() { root.prob_plot_group = $(this).val(); return redraw_prob_plot(); }); - make_table(); - edit_data_change(); + $('.stats_panel').click(function() { + make_table(); + edit_data_change(); + }); $('#edit_sample_lists').change(edit_data_change); $('.edit_sample_value').change(edit_data_change); $('#block_by_index').click(edit_data_change); diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js index daa5b3f2..4e82fff2 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js +++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js @@ -154,36 +154,12 @@ }; })(this)); - $("#pylmm_mapping_compute").on("mouseover", (function(_this) { - return function() { - if ($(".outlier").length && $(".outlier-alert").length < 1) { - return showalert(outlier_text, "alert-success outlier-alert"); - } - }; - })(this)); - - $("#pylmm_compute").on("click", (function(_this) { - return function() { - var form_data, url; - //$("#progress_bar_container").modal(); - url = "/loading"; - $('input[name=method]').val("pylmm"); - $('input[name=genofile]').val($('#genofile_pylmm').val()); - $('input[name=num_perm]').val($('input[name=num_perm_pylmm]').val()); - $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_pylmm]:checked').val()); - form_data = $('#trait_data_form').serialize(); - console.log("form_data is:", form_data); - return submit_special(url); - //return do_ajax_post(url, form_data); - }; - })(this)); - $("#rqtl_geno_compute").on("click", (function(_this) { return function() { var form_data, url; - //$("#progress_bar_container").modal(); url = "/loading"; $('input[name=method]').val("rqtl_geno"); + $('input[name=selected_chr]').val($('#chr_rqtl_geno').val()); $('input[name=genofile]').val($('#genofile_rqtl_geno').val()); $('input[name=num_perm]').val($('input[name=num_perm_rqtl_geno]').val()); $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_rqtl]:checked').val()); @@ -203,7 +179,6 @@ } else { return submit_special(url); - //return do_ajax_post(url, form_data); } }; })(this)); @@ -214,6 +189,7 @@ console.log("RUNNING GEMMA"); url = "/loading"; $('input[name=method]').val("gemma"); + $('input[name=selected_chr]').val($('#chr_gemma').val()); $('input[name=num_perm]').val(0); $('input[name=genofile]').val($('#genofile_gemma').val()); $('input[name=maf]').val($('input[name=maf_gemma]').val()); @@ -230,6 +206,7 @@ //$("#progress_bar_container").modal(); url = "/loading"; $('input[name=method]').val("reaper"); + $('input[name=selected_chr]').val($('#chr_reaper').val()); $('input[name=genofile]').val($('#genofile_reaper').val()); $('input[name=num_perm]').val($('input[name=num_perm_reaper]').val()); $('input[name=control_marker]').val($('input[name=control_reaper]').val()); diff --git a/wqflask/wqflask/static/new/javascript/stats.js b/wqflask/wqflask/static/new/javascript/stats.js index 4f99982e..356d1cb0 100644 --- a/wqflask/wqflask/static/new/javascript/stats.js +++ b/wqflask/wqflask/static/new/javascript/stats.js @@ -154,16 +154,4 @@ Stats = (function() { })(); -bxd_only = new Stats([3, 5, 7, 8]); - -console.log("[xred] bxd_only mean:", bxd_only.mean()); - -console.log("[xgreen] bxd_only median:", bxd_only.median()); - -console.log("[xpurple] bxd_only std_dev:", bxd_only.std_dev()); - -console.log("[xmagenta] bxd_only std_error:", bxd_only.std_error()); - -console.log("[xyellow] bxd_only min:", bxd_only.min()); - window.Stats = Stats; diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html index 5fb2c95e..00d725ea 100644 --- a/wqflask/wqflask/templates/mapping_results.html +++ b/wqflask/wqflask/templates/mapping_results.html @@ -257,7 +257,7 @@ <div style="width: 100%;"> <h2>Interval Analyst</h2> <div id="table_container"> - <table id="interval_analyst" class="table table-hover table-striped nowrap"> + <table id="interval_analyst" class="table-hover table-striped cell-border" style="float: left; width:100%;"> <thead> <tr> {% for header in gene_table_header %} @@ -355,9 +355,7 @@ "autoWidth": false, "deferRender": true, "bSortClasses": false, - "scrollY": "600px", "scrollCollapse": false, - "scroller": true, "paging": false } ); @@ -372,7 +370,6 @@ "autoWidth": false, "deferRender": true, "bSortClasses": false, - "scrollY": "600px", "scrollCollapse": false, "paging": false } ); diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index 9ad8a53e..a325ec9f 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -4,6 +4,7 @@ <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" /> <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/scroller.dataTables.min.css"> <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.dataTables.css"> + <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" /> {% endblock %} {% block content %} <!-- Start of body --> @@ -84,9 +85,9 @@ <th></th> {% for header in header_fields %} {% if header == 'Max LRS' %} - <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#LRS" target="_blank"><img style="width: 15px; height: 15px;" src="/static/new/images/question_mark.jpg"></a></th> + <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#LRS" target="_blank" style="color: white;"><sup>?</sup></a></th> {% elif header == 'Additive Effect' %} - <th data-export="Additive Effect">Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank"><img style="width: 15px; height: 15px;" src="/static/new/images/question_mark.jpg"></a></th> + <th data-export="Additive Effect">Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank" style="color: white;"><sup>?</sup></a></th> {% else %} <th data-export="{{header}}">{{header}}</th> {% endif %} @@ -99,9 +100,9 @@ <th></th> {% for header in header_fields %} {% if header == 'Max LRS' %} - <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#LRS" target="_blank"><img style="width: 15px; height: 15px;" src="/static/new/images/question_mark.jpg"></a></th> + <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#LRS" target="_blank" style="color: white;"><sup>?</sup></a></th> {% elif header == 'Additive Effect' %} - <th data-export="Additive Effect">Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank"><img style="width: 15px; height: 15px;" src="/static/new/images/question_mark.jpg"></a></th> + <th data-export="Additive Effect">Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank" style="color: white;"><sup>?</sup></a></th> {% else %} <th data-export="{{header}}">{{header}}</th> {% endif %} diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index 8726226c..f5e81060 100644 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -52,7 +52,7 @@ </div> </div> <div class="panel panel-default"> - <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseTwo"> + <div class="panel-heading stats_panel" data-toggle="collapse" data-parent="#accordion" data-target="#collapseTwo"> <h3 class="panel-title"> <span class="glyphicon glyphicon-chevron-down"></span> Statistics </h3> @@ -62,26 +62,38 @@ {% include 'show_trait_statistics.html' %} </div> </div> - </div> + </div> <div class="panel panel-default"> <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseThree"> <h3 class="panel-title"> - <span class="glyphicon glyphicon-chevron-down"></span> Calculate Correlations + <span class="glyphicon glyphicon-chevron-down"></span> Transform and Filter Data </h3> </div> <div id="collapseThree" class="panel-collapse collapse in"> <div class="panel-body"> + {% include 'show_trait_transform_and_filter.html' %} + </div> + </div> + </div> + <div class="panel panel-default"> + <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseFour"> + <h3 class="panel-title"> + <span class="glyphicon glyphicon-chevron-down"></span> Calculate Correlations + </h3> + </div> + <div id="collapseFour" class="panel-collapse collapse in"> + <div class="panel-body"> {% include 'show_trait_calculate_correlations.html' %} </div> </div> </div> <div class="panel panel-default"> - <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseFour"> + <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseFive"> <h3 class="panel-title"> <span class="glyphicon glyphicon-chevron-down"></span> Mapping Tools </h3> </div> - <div id="collapseFour" class="panel-collapse collapse in"> + <div id="collapseFive" class="panel-collapse collapse in"> <div class="panel-body"> {% include 'show_trait_mapping_tools.html' %} </div> @@ -89,12 +101,12 @@ </div> </div> <div class="panel panel-default"> - <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseFive" aria-expanded="true"> + <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseSix" aria-expanded="true"> <h3 class="panel-title"> <span class="glyphicon glyphicon-chevron-up"></span> Review and Edit Data </h3> </div> - <div id="collapseFive" class="panel-collapse collapse" aria-expanded="true"> + <div id="collapseSix" class="panel-collapse collapse" aria-expanded="true"> <div class="panel-body"> {% include 'show_trait_edit_data.html' %} </div> @@ -210,7 +222,7 @@ "iDisplayLength": -1, "autoWidth": true, "bLengthChange": true, - "bDeferRender": true, + "deferRender": false, "bSortClasses": false, "scrollY": "600px", "scrollCollapse": false, @@ -221,7 +233,7 @@ } ); {% else %} - + $('#samples_primary, #samples_other').DataTable( { "columns": [ { "bSortable": false, "width": "8%" }, @@ -242,7 +254,7 @@ "iDisplayLength": -1, "autoWidth": true, "bLengthChange": true, - "bDeferRender": true, + "deferRender": false, "bSortClasses": false, "scrollY": "600px", "scrollCollapse": false, @@ -251,6 +263,7 @@ }, "paging": false } ); + {% endif %} var slider = document.getElementById('p_range_slider'); diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html index c1f8f824..0192bff1 100644 --- a/wqflask/wqflask/templates/show_trait_details.html +++ b/wqflask/wqflask/templates/show_trait_details.html @@ -5,10 +5,6 @@ </tr> {% if this_trait.dataset.type == 'Publish' %} <tr> - <td>Tissue</td> - <td>{{ this_trait.dataset.tissue }}</td> - </tr> - <tr> <td>Phenotype</td> <td><div style="width:40%;">{{ this_trait.description_fmt }}</div></td> </tr> @@ -24,6 +20,11 @@ <td>Journal</td> <td>{{ this_trait.journal }} (<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids={{ this_trait.pubmed_id }}&dop=Abstract" title="PubMed">{{ this_trait.year }}</a>)</td> </tr> + {% else %} + <tr> + <td>Tissue</td> + <td>{{ this_trait.dataset.tissue }}</td> + </tr> {% endif %} {% if this_trait.dataset.type == 'ProbeSet' %} {% if this_trait.symbol != None %} diff --git a/wqflask/wqflask/templates/show_trait_edit_data.html b/wqflask/wqflask/templates/show_trait_edit_data.html index cfcf2ce5..ab134663 100644 --- a/wqflask/wqflask/templates/show_trait_edit_data.html +++ b/wqflask/wqflask/templates/show_trait_edit_data.html @@ -1,6 +1,7 @@ <div> <!--<h2>Review and Edit Data</h2>--> +<!-- <div class="well form-horizontal"> <fieldset id="showHideOptions"> <legend>Block samples</legend> @@ -59,11 +60,6 @@ <option value="sqrt">Square Root</option> </select> </div> - <!-- - {% if sample_groups[0].sample_qnorm is not none %} - <input type="button" id="qnorm" class="btn btn-default" value="Quantile Normalize"> - {% endif %} - --> </div> </fieldset> <br> @@ -81,7 +77,7 @@ </div> </div> <br> - +--> <!--<div id="edit_sample_lists">--> {% for sample_type in sample_groups %} @@ -94,7 +90,7 @@ <thead> <tr> <th></th> - <th>Index</th> + <th>ID</th> <th>Sample</th> <th style="text-align: right;">Value</th> {% if sample_type.se_exists() %} @@ -113,7 +109,7 @@ </thead> <tbody> {% for sample in sample_type.sample_list %} - <tr class="{{ sample.class_outlier }} value_se" id="{{ sample.this_id }}"> + <tr class="{{ sample.class_outlier }} value_se" id="{% if outer_loop.index == 1 %}Primary_{{ sample.this_id }}{% else %}Other_{{ sample.this_id }}{% endif %}"> <td align="center" style="padding-left: 0px; padding-right: 0px;" class="column_name-"><input type="checkbox" name="selectCheck" class="checkbox edit_sample_checkbox" value="{{ sample.name }}" checked="checked"> </td> <td class="column_name-Index" align="right">{{ loop.index }}</td> diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index 8e003897..e0bc8eb8 100644 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html @@ -14,11 +14,6 @@ <li> <a href="#rqtl_geno" data-toggle="tab">R/qtl</a> </li> -<!-- - <li> - <a href="#pylmm" data-toggle="tab">pyLMM</a> - </li> ---> {% endif %} {% for mapping_method in dataset.group.mapping_names %} {% if mapping_method == "GEMMA" %} @@ -39,6 +34,16 @@ <div class="tab-content"> <div class="tab-pane active" id="gemma"> <div style="padding-top: 20px;" class="form-horizontal"> + <div class="mapping_method_fields form-group"> + <label for="chr_select" style="text-align: right;" class="col-xs-3 control-label">Chromosome</label> + <div style="margin-left:20px;" class="col-xs-2 controls"> + <select id="chr_gemma" class="form-control"> + {% for item in chr_list %} + <option value="{{ item[1] }}">{{ item[0] }}</option> + {% endfor %} + </select> + </div> + </div> {% if genofiles and genofiles|length>0 %} <div class="mapping_method_fields form-group"> <label for="genofiles" style="text-align: right;" class="col-xs-3 control-label">Genotypes</label> @@ -61,11 +66,11 @@ <label style="text-align: right;" class="col-xs-3 control-label">Use LOCO</label> <div style="margin-left:20px;" class="col-xs-6 controls"> <label class="radio-inline"> - <input type="radio" name="use_loco" value="True"> + <input type="radio" name="use_loco" value="True" checked=""> Yes </label> <label class="radio-inline"> - <input type="radio" name="use_loco" value="False" checked=""> + <input type="radio" name="use_loco" value="False"> No </label> </div> @@ -110,6 +115,16 @@ {% if dataset.group.mapping_id == "1" %} <div class="tab-pane" id="interval_mapping"> <div style="margin-top: 20px" class="form-horizontal"> + <div class="mapping_method_fields form-group"> + <label for="chr_select" style="text-align: right;" class="col-xs-3 control-label">Chromosome</label> + <div style="margin-left:20px;" class="col-xs-2 controls"> + <select id="chr_reaper" class="form-control"> + {% for item in chr_list %} + <option value="{{ item[1] }}">{{ item[0] }}</option> + {% endfor %} + </select> + </div> + </div> {% if genofiles and genofiles|length>0 %} <div class="mapping_method_fields form-group"> <label style="text-align: right;" for="genofiles" class="col-xs-3 control-label">Genotypes</label> @@ -202,6 +217,16 @@ </div> <div class="tab-pane" id="rqtl_geno"> <div style="margin-top: 20px" class="form-horizontal"> + <div class="mapping_method_fields form-group"> + <label for="chr_select" style="text-align: right;" class="col-xs-3 control-label">Chromosome</label> + <div style="margin-left:20px;" class="col-xs-2 controls"> + <select id="chr_rqtl_geno" class="form-control"> + {% for item in chr_list %} + <option value="{{ item[1] }}">{{ item[0] }}</option> + {% endfor %} + </select> + </div> + </div> {% if genofiles and genofiles|length>0 %} <div class="mapping_method_fields form-group"> <label style="text-align:right;" for="genofiles" class="col-xs-3 control-label">Genotypes</label> @@ -304,30 +329,6 @@ </div> </div> </div> - <div class="tab-pane" id="pylmm"> - <div style="margin-top: 20px" class="form-horizontal"> - {% if genofiles and genofiles|length>0 %} - <div class="mapping_method_fields form-group"> - <label style="text-align:right;" class="col-xs-3 control-label">Genotypes</label> - <div style="margin-left: 20px;" class="col-xs-4 controls"> - <select id="genofile_pylmm" class="form-control"> - {% for item in genofiles %} - <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option> - {% endfor %} - </select> - </div> - </div> - {% endif %} - <div class="mapping_method_fields form-group"> - <label class="col-xs-3 control-label"></label> - <div style="margin-left:20px;" class="col-xs-6"> - <button id="pylmm_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Interval Mapping"> - Compute - </button> - </div> - </div> - </div> - </div> {% endif %} </div> </div> @@ -341,10 +342,6 @@ <dd>Interval mapping is a process in which the statistical significance of a hypothetical QTL is evaluated at regular points across a chromosome, even in the absence of explicit genotype data at those points.</dd> <dt>R/qtl</dt> <dd>R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTL) in experimental crosses.</dd> -<!-- - <dt>pyLMM</dt> - <dd>pyLMM is a fast and lightweight linear mixed-model (LMM) solver for use in genome-wide association studies (GWAS).</dd> ---> {% endif %} </dl> </div> diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html index ac0c753a..a0bdc987 100644 --- a/wqflask/wqflask/templates/show_trait_statistics.html +++ b/wqflask/wqflask/templates/show_trait_statistics.html @@ -5,15 +5,15 @@ <a href="#stats_tab" data-toggle="tab">Basic Statistics</a> </li> <li> - <a href="#histogram_tab" data-toggle="tab">Histogram</a> + <a href="#histogram_tab" class="histogram_tab" data-toggle="tab">Histogram</a> </li> {% if num_values < 256 %} <li> - <a href="#bar_chart_tab" data-toggle="tab">Bar Chart</a> + <a href="#bar_chart_tab" class="bar_chart_tab" data-toggle="tab">Bar Chart</a> </li> {% endif %} <li> - <a href="#probability_plot" data-toggle="tab">Probability Plot</a> + <a href="#probability_plot" class="prob_plot_tab" data-toggle="tab">Probability Plot</a> </li> {% if g.user_session.logged_in %} <li> @@ -21,10 +21,10 @@ </li> {% endif %} <li> - <a href="#box_plot_tab" data-toggle="tab">Box Plot</a> + <a href="#box_plot_tab" class="box_plot_tab" data-toggle="tab">Box Plot</a> </li> <li> - <a href="#violin_plot_tab" data-toggle="tab">Violin Plot</a> + <a href="#violin_plot_tab" class="violin_plot_tab" data-toggle="tab">Violin Plot</a> </li> </ul> diff --git a/wqflask/wqflask/templates/show_trait_transform_and_filter.html b/wqflask/wqflask/templates/show_trait_transform_and_filter.html new file mode 100644 index 00000000..5d14a30e --- /dev/null +++ b/wqflask/wqflask/templates/show_trait_transform_and_filter.html @@ -0,0 +1,79 @@ +<div> + <div class="form-horizontal"> + <legend>Block samples</legend> + <p>Edit or delete values in the Trait Data boxes, and use the + <strong>Reset</strong> option as + needed. + </p> + + <div id="blockMenuSpan" class="input-append" style="margin-bottom: 10px;"> + <label for="remove_samples_field">Block samples by index:</label> + <input type="text" id="remove_samples_field"> + <select id="block_group" size="1"> + <option value="primary"> + {{ sample_group_types['samples_primary'] }} + </option> + <option value="other"> + {{ sample_group_types['samples_other'] }} + </option> + </select> + <input type="button" id="block_by_index" class="btn" value="Block"> + </div> + <div id="remove_samples_invalid" class="alert alert-error" style="display:none;"> + Please check that your input is formatted correctly, e.g. <strong>3, 5-10, 12</strong> + </div> + {% if sample_groups[0].attributes %} + <div class="input-append" style="margin-top:10px; margin-bottom:10px;"> + <label for="exclude_menu">Block samples by group:</label> + <select id="exclude_menu" size=1> + {% for attribute in sample_groups[0].attributes %} + <option value="{{ sample_groups[0].attributes[attribute].name.replace(' ', '_') }}"> + {{ sample_groups[0].attributes[attribute].name }}</option> + {% endfor %} + </select> + <select id="attribute_values" size=1> + </select> + <input type="button" id="exclude_group" class="btn" value="Block"> + </div> + {% endif %} + <div> + <input 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" id="reset" class="btn btn-primary" value="Reset"> + <span class="input-append"> + <input type="button" id="export" class="btn btn-default" value="Export"> + <select id="export_format" class="select optional span2"> + <option value="excel">Excel</option> + <option value="csv">CSV</option> + </select> + </span> + <br> + <div style="margin-top:10px;"> + <input type="button" id="normalize" class="btn btn-default" value="Normalize"> + <select id="norm_method" class="select optional span2"> + <option value="log2">Log2</option> + <option value="qnorm">Quantile</option> + <option value="sqrt">Square Root</option> + </select> + </div> + <!-- + {% if sample_groups[0].sample_qnorm is not none %} + <input type="button" id="qnorm" class="btn btn-default" value="Quantile Normalize"> + {% endif %} + --> + </div> + <br> + + <div> + <p>Outliers highlighted in + <strong style="background-color:yellow;">yellow</strong> + can be hidden using + the <strong>Hide Outliers</strong> button. + </p> + + <p>Samples with no value (x) can be hidden by clicking + <strong>Hide No Value</strong> button. + </p> + </div> + </div> +</div> \ No newline at end of file |