From 36ceda09d76c898c5f818236122f5d431261a5b1 Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 23 Apr 2018 16:19:24 +0000 Subject: Changed GEMMA mapping to use -lmm 2 (Likelihood ratio test) as a parameter instead of -lmm 1 (Wald test) Added script to convert .geno files to JSON to maintenance folder (geno_to_json.py) --- wqflask/maintenance/geno_to_json.py | 195 ++++++++++++++++++++++++++++++++++++ 1 file changed, 195 insertions(+) create mode 100644 wqflask/maintenance/geno_to_json.py (limited to 'wqflask/maintenance/geno_to_json.py') diff --git a/wqflask/maintenance/geno_to_json.py b/wqflask/maintenance/geno_to_json.py new file mode 100644 index 00000000..789a1691 --- /dev/null +++ b/wqflask/maintenance/geno_to_json.py @@ -0,0 +1,195 @@ +#!/usr/bin/python + +""" +Convert .geno files to json + +This file goes through all of the genofiles in the genofile directory (.geno) +and converts them to json files that are used when running the marker regression +code + +""" + +from __future__ import print_function, division, absolute_import +import sys +sys.path.append("..") +import os +import glob +import traceback +import gzip + +#import numpy as np +#from pyLMM import lmm + +import simplejson as json + +from pprint import pformat as pf + +class EmptyConfigurations(Exception): pass + + + +class Marker(object): + def __init__(self): + self.name = None + self.chr = None + self.cM = None + self.Mb = None + self.genotypes = [] + +class ConvertGenoFile(object): + + def __init__(self, input_file, output_file): + + self.input_file = input_file + self.output_file = output_file + + self.mb_exists = False + self.cm_exists = False + self.markers = [] + + self.latest_row_pos = None + self.latest_col_pos = None + + self.latest_row_value = None + self.latest_col_value = None + + def convert(self): + + self.haplotype_notation = { + '@mat': "1", + '@pat': "0", + '@het': "0.5", + '@unk': "NA" + } + + self.configurations = {} + #self.skipped_cols = 3 + + #if self.input_file.endswith(".geno.gz"): + # print("self.input_file: ", self.input_file) + # self.input_fh = gzip.open(self.input_file) + #else: + self.input_fh = open(self.input_file) + + with open(self.output_file, "w") as self.output_fh: + #if self.file_type == "geno": + self.process_csv() + #elif self.file_type == "snps": + # self.process_snps_file() + + + def process_csv(self): + for row_count, row in enumerate(self.process_rows()): + row_items = row.split("\t") + + this_marker = Marker() + this_marker.name = row_items[1] + this_marker.chr = row_items[0] + if self.cm_exists and self.mb_exists: + this_marker.cM = row_items[2] + this_marker.Mb = row_items[3] + genotypes = row_items[4:] + elif self.cm_exists: + this_marker.cM = row_items[2] + genotypes = row_items[3:] + elif self.mb_exists: + this_marker.Mb = row_items[2] + genotypes = row_items[3:] + else: + genotypes = row_items[2:] + for item_count, genotype in enumerate(genotypes): + if genotype.upper() in self.configurations: + this_marker.genotypes.append(self.configurations[genotype.upper()]) + else: + this_marker.genotypes.append("NA") + + #print("this_marker is:", pf(this_marker.__dict__)) + #if this_marker.chr == "14": + self.markers.append(this_marker.__dict__) + + with open(self.output_file, 'w') as fh: + json.dump(self.markers, fh, indent=" ", sort_keys=True) + + # print('configurations:', str(configurations)) + #self.latest_col_pos = item_count + self.skipped_cols + #self.latest_col_value = item + + #if item_count != 0: + # self.output_fh.write(" ") + #self.output_fh.write(self.configurations[item.upper()]) + + #self.output_fh.write("\n") + + + def process_rows(self): + for self.latest_row_pos, row in enumerate(self.input_fh): + #if self.input_file.endswith(".geno.gz"): + # print("row: ", row) + self.latest_row_value = row + # Take care of headers + if not row.strip(): + continue + if row.startswith('#'): + continue + if row.startswith('Chr'): + if 'Mb' in row.split(): + self.mb_exists = True + if 'cM' in row.split(): + self.cm_exists = True + continue + if row.startswith('@'): + key, _separater, value = row.partition(':') + key = key.strip() + value = value.strip() + if key in self.haplotype_notation: + self.configurations[value] = self.haplotype_notation[key] + continue + if not len(self.configurations): + raise EmptyConfigurations + yield row + + @classmethod + def process_all(cls, old_directory, new_directory): + os.chdir(old_directory) + for input_file in glob.glob("*"): + if not input_file.endswith(('geno', '.geno.gz')): + continue + group_name = ".".join(input_file.split('.')[:-1]) + output_file = os.path.join(new_directory, group_name + ".json") + print("%s -> %s" % ( + os.path.join(old_directory, input_file), output_file)) + convertob = ConvertGenoFile(input_file, output_file) + try: + convertob.convert() + except EmptyConfigurations as why: + print(" No config info? Continuing...") + #excepted = True + continue + except Exception as why: + + print(" Exception:", why) + print(traceback.print_exc()) + print(" Found in row %s at tabular column %s" % (convertob.latest_row_pos, + convertob.latest_col_pos)) + print(" Column is:", convertob.latest_col_value) + print(" Row is:", convertob.latest_row_value) + break + + #def process_snps_file(cls, snps_file, new_directory): + # output_file = os.path.join(new_directory, "mouse_families.json") + # print("%s -> %s" % (snps_file, output_file)) + # convertob = ConvertGenoFile(input_file, output_file) + + + +if __name__=="__main__": + Old_Geno_Directory = """/home/zas1024/genotype_files/genotype/""" + New_Geno_Directory = """/home/zas1024/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") + #convertob.convert() + ConvertGenoFile.process_all(Old_Geno_Directory, New_Geno_Directory) + #ConvertGenoFiles(Geno_Directory) + + #process_csv(Input_File, Output_File) \ No newline at end of file -- cgit v1.2.3 From dc3bc97b2ae2e751f68ad63359734d569895c711 Mon Sep 17 00:00:00 2001 From: zsloan Date: Tue, 20 Nov 2018 12:08:47 -0600 Subject: Added option to select chromosome from trait page when mapping Put transform/blocking tools into their own tab (still need to change formatting of tab's contents) Improved appearance of search result page table (still need to change a few other tables) Fixed issue that caused parent/f1 strains to not be blocked correctly when using "block by index" tool Basic Stats figures now load when the user clicks the tab, to improve initial page load time --- bin/genenetwork2 | 2 +- .../maintenance/generate_kinship_from_bimbam.py | 4 +- wqflask/maintenance/geno_to_json.py | 6 +- wqflask/wqflask/show_trait/SampleList.py | 5 +- wqflask/wqflask/show_trait/show_trait.py | 8 +- wqflask/wqflask/static/new/css/show_trait.css | 4 + .../new/javascript/dataset_menu_structure.json | 96 +++++++++++++++++++--- .../wqflask/static/new/javascript/show_trait.js | 80 +++++++++++++----- .../new/javascript/show_trait_mapping_tools.js | 29 +------ wqflask/wqflask/static/new/javascript/stats.js | 12 --- wqflask/wqflask/templates/mapping_results.html | 5 +- wqflask/wqflask/templates/search_result_page.html | 9 +- wqflask/wqflask/templates/show_trait.html | 33 +++++--- wqflask/wqflask/templates/show_trait_details.html | 9 +- .../wqflask/templates/show_trait_edit_data.html | 12 +-- .../templates/show_trait_mapping_tools.html | 67 ++++++++------- .../wqflask/templates/show_trait_statistics.html | 10 +-- .../templates/show_trait_transform_and_filter.html | 79 ++++++++++++++++++ 18 files changed, 323 insertions(+), 147 deletions(-) create mode 100644 wqflask/wqflask/templates/show_trait_transform_and_filter.html (limited to 'wqflask/maintenance/geno_to_json.py') 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": [ [ @@ -2590,6 +2626,11 @@ ] ], "Liver mRNA": [ + [ + "857", + "EPFLMouseLiverCDHFDRMA0818", + "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA" + ], [ "859", "EPFLMouseLiverCDRMA0818", @@ -2620,11 +2661,6 @@ "NIA-AgBXD-Liv_HFD-0818", "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", @@ -2640,6 +2676,11 @@ "EPFLMouseLiverCDRMA0413", "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", @@ -2650,11 +2691,6 @@ "EPFLMouseLiverCDEx0413", "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", @@ -4001,6 +4037,22 @@ "AIL", "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 @@

Interval Analyst

- +
{% 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 @@ + {% endblock %} {% block content %} @@ -84,9 +85,9 @@ {% for header in header_fields %} {% if header == 'Max LRS' %} - + {% elif header == 'Additive Effect' %} - + {% else %} {% endif %} @@ -99,9 +100,9 @@ {% for header in header_fields %} {% if header == 'Max LRS' %} - + {% elif header == 'Additive Effect' %} - + {% else %} {% 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 @@
-
+

Statistics

@@ -62,26 +62,38 @@ {% include 'show_trait_statistics.html' %}
-
+

- Calculate Correlations + Transform and Filter Data

+
+ {% include 'show_trait_transform_and_filter.html' %} +
+
+
+
+
+

+ Calculate Correlations +

+
+
{% include 'show_trait_calculate_correlations.html' %}
-
+

Mapping Tools

-
+
{% include 'show_trait_mapping_tools.html' %}
@@ -89,12 +101,12 @@
-
+

Review and Edit Data

-
+
{% include 'show_trait_edit_data.html' %}
@@ -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 @@ -4,10 +4,6 @@
{% if this_trait.dataset.type == 'Publish' %} - - - - @@ -24,6 +20,11 @@ + {% else %} + + + + {% 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 @@
+

@@ -81,7 +77,7 @@
- +--> {% for sample_type in sample_groups %} @@ -94,7 +90,7 @@ - + {% if sample_type.se_exists() %} @@ -113,7 +109,7 @@ {% for sample in sample_type.sample_list %} - + 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 @@
  • R/qtl
    • - {% endif %} {% for mapping_method in dataset.group.mapping_names %} {% if mapping_method == "GEMMA" %} @@ -39,6 +34,16 @@
    +
    + +
    + +
    +
    {% if genofiles and genofiles|length>0 %}
    @@ -61,11 +66,11 @@
    @@ -110,6 +115,16 @@ {% if dataset.group.mapping_id == "1" %}
    +
    + +
    + +
    +
    {% if genofiles and genofiles|length>0 %}
    @@ -202,6 +217,16 @@
    +
    + +
    + +
    +
    {% if genofiles and genofiles|length>0 %}
    @@ -304,30 +329,6 @@
    -
    -
    - {% if genofiles and genofiles|length>0 %} -
    - -
    - -
    -
    - {% endif %} -
    - -
    - -
    -
    -
    -
    {% endif %}
    @@ -341,10 +342,6 @@
    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.
    R/qtl
    R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTL) in experimental crosses.
    - {% endif %}
    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 @@ Basic Statistics
  • - Histogram + Histogram
    • {% if num_values < 256 %}
  • - Bar Chart + Bar Chart
    • {% endif %}
  • - Probability Plot + Probability Plot
    • {% if g.user_session.logged_in %}
  • @@ -21,10 +21,10 @@
    • {% endif %}
  • - Box Plot + Box Plot
  • - Violin Plot + Violin Plot
    • 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 @@ +
    +
    + Block samples +

    Edit or delete values in the Trait Data boxes, and use the + Reset option as + needed. +

    + +
    + + + + +
    + + {% if sample_groups[0].attributes %} +
    + + + + +
    + {% endif %} +
    + + + + + + + +
    +
    + + +
    + +
    +
    + +
    +

    Outliers highlighted in + yellow + can be hidden using + the Hide Outliers button. +

    + +

    Samples with no value (x) can be hidden by clicking + Hide No Value button. +

    +
    +
    +
    \ No newline at end of file -- cgit v1.2.3
    Max LRS Max LRS ?Additive Effect Additive Effect ?{{header}}Max LRS Max LRS ?Additive Effect Additive Effect ?{{header}} {{ this_trait.dataset.group.species }}, {{ this_trait.dataset.group.name }}
    Tissue{{ this_trait.dataset.tissue }}
    Phenotype
    {{ this_trait.description_fmt }}
    		Journal {{ this_trait.journal }} ({{ this_trait.year }})
    Tissue{{ this_trait.dataset.tissue }}
    IndexID Sample Value
    {{ loop.index }}