diff options
| -rw-r--r-- | wqflask/wqflask/correlation/show_corr_results.py | 74 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/gemma_mapping.py | 18 | ||||
| -rw-r--r-- | wqflask/wqflask/static/dbdoc/TODO.md | 1 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/correlation_page.html | 86 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/empty_collection.html | 15 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 2 |
6 files changed, 169 insertions, 27 deletions
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 3d1c0d17..9b048346 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -32,6 +32,7 @@ import pp import math import collections import resource +import json import scipy @@ -51,6 +52,7 @@ import utility.webqtlUtil #this is for parallel computing only. from wqflask.correlation import correlation_functions from utility.benchmark import Bench import utility.webqtlUtil +from wqflask import user_manager from MySQLdb import escape_string as escape @@ -248,7 +250,7 @@ class CorrelationResults(object): else: self.this_trait_vals.append("None") num_overlap = len(self.this_trait_vals) - + logger.debug("DOING PARALLEL") self.do_parallel_correlation(db_filename, num_overlap) else: for trait, values in self.target_dataset.trait_data.iteritems(): @@ -335,6 +337,7 @@ class CorrelationResults(object): #print("self.correlation_results: ", pf(self.correlation_results)) + self.json_results = generate_corr_json(self.correlation_results, self.this_trait, self.dataset, self.target_dataset) #XZ, 09/18/2008: get all information about the user selected database. #target_db_name = fd.corr_dataset @@ -1195,6 +1198,17 @@ class CorrelationResults(object): import math import reaper + def cmpOrder2(A,B): + try: + if A[-1] < B[-1]: + return -1 + elif A[-1] == B[-1]: + return 0 + else: + return 1 + except: + return 0 + def calCorrelation(dbdata,userdata,N): X = [] Y = [] @@ -1420,3 +1434,61 @@ class CorrelationResults(object): # for one_result in results: # for one_traitinfo in one_result: # allcorrelations.append( one_traitinfo ) + +def generate_corr_json(corr_results, this_trait, dataset, target_dataset): + results_list = [] + for i, trait in enumerate(corr_results): + results_dict = {} + results_dict['checkbox'] = "<INPUT TYPE='checkbox' NAME='searchResult' class='checkbox trait_checkbox' style='padding-right: 0px;' VALUE='" + user_manager.data_hmac('{}:{}'.format(trait.name, trait.dataset.name)) + "'>" + results_dict['index'] = i + 1 + results_dict['trait_id'] = "<a href='/show_trait?trait_id="+str(trait.name)+"&dataset="+str(dataset.name)+"'>"+str(trait.name)+"</a>" + if target_dataset.type == "ProbeSet": + results_dict['symbol'] = trait.symbol + results_dict['description'] = trait.description_display + results_dict['location'] = trait.location_repr + results_dict['mean'] = float(trait.mean) + if trait.LRS_score_repr != "N/A": + results_dict['lrs_score'] = "%.1f" % float(trait.LRS_score_repr) + else: + results_dict['lrs_score'] = "N/A" + results_dict['lrs_location'] = trait.LRS_location_repr + if trait.additive != "": + results_dict['additive'] = "%0.3f" % float(trait.additive) + else: + results_dict['additive'] = "N/A" + results_dict['sample_r'] = "<a target='_blank' href='corr_scatter_plot?dataset_1=" + str(dataset.name) + "&dataset_2=" + str(trait.dataset.name) + "&trait_1=" + str(this_trait.name) + "&trait_2=" + str(trait.name) + "'>" + "%0.3f" % float(trait.sample_r) + "</a>" + results_dict['num_overlap'] = trait.num_overlap + results_dict['sample_p'] = "%0.3e" % float(trait.sample_p) + if trait.lit_corr == "" or trait.lit_corr == 0: + results_dict['lit_corr'] = "--" + else: + results_dict['lit_corr'] = "%0.3f" % float(trait.lit_corr) + if trait.tissue_corr == "" or trait.tissue_corr == 0: + results_dict['tissue_corr'] = "--" + else: + results_dict['tissue_corr'] = "%0.3f" % float(trait.tissue_corr) + elif target_dataset.type == "Publish": + results_dict['description'] = trait.description_display + results_dict['authors'] = trait.authors + if trait.pubmed_id: + results_dict['pubmed'] = "<a href='" + trait.pubmed_link + "'> " + trait.pubmed_text + "</a>" + else: + results_dict['pubmed'] = "N/A" + results_dict['lrs_score'] = trait.LRS_score_repr + results_dict['lrs_location'] = trait.LRS_location_repr + if trait.additive != "": + results_dict['additive'] = "%0.3f" % float(trait.additive) + else: + results_dict['additive'] = "N/A" + results_dict['sample_r'] = "<a target='_blank' href='corr_scatter_plot?dataset_1=" + str(dataset.name) + "&dataset_2=" + str(trait.dataset.name) + "&trait_1=" + str(this_trait.name) + "&trait_2=" + str(trait.name) + "'>" + "%0.3f" % trait.sample_r + "</a>" + results_dict['num_overlap'] = trait.num_overlap + results_dict['sample_p'] = "%0.3e" % float(trait.sample_p) + else: + results_dict['lrs_location'] = trait.LRS_location_repr + results_dict['sample_r'] = "<a target='_blank' href='corr_scatter_plot?dataset_1=" + str(dataset.name) + "&dataset_2=" + str(trait.dataset.name) + "&trait_1=" + str(this_trait.name) + "&trait_2=" + str(trait.name) + "'>" + "%0.3f" % float(trait.sample_r) + "</a>" + results_dict['num_overlap'] = trait.num_overlap + results_dict['sample_p'] = "%0.3e" % float(trait.sample_p) + + results_list.append(results_dict) + + return json.dumps(results_list) diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index 68920130..233a5c76 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -3,7 +3,7 @@ import os, math, string, random, json from base import webqtlConfig from base.trait import GeneralTrait from base.data_set import create_dataset -from utility.tools import flat_files, GEMMA_COMMAND, GEMMA_WRAPPER_COMMAND, TEMPDIR, assert_bin, assert_file +from utility.tools import flat_files, GEMMA_COMMAND, GEMMA_WRAPPER_COMMAND, TEMPDIR import utility.logger logger = utility.logger.getLogger(__name__ ) @@ -11,7 +11,6 @@ logger = utility.logger.getLogger(__name__ ) def run_gemma(this_dataset, samples, vals, covariates, method, use_loco): """Generates p-values for each marker using GEMMA""" - assert_bin(GEMMA_COMMAND); if this_dataset.group.genofile != None: genofile_name = this_dataset.group.genofile[:-5] else: @@ -193,7 +192,7 @@ def parse_gemma_output(genofile_name): # if marker['chr'] != previous_chr: # previous_chr = marker['chr'] marker['Mb'] = float(line.split("\t")[2]) / 1000000 - marker['p_value'] = float(line.split("\t")[10]) + marker['p_value'] = float(line.split("\t")[11]) if math.isnan(marker['p_value']) or (marker['p_value'] <= 0): marker['lod_score'] = 0 #marker['lrs_value'] = 0 @@ -203,20 +202,15 @@ def parse_gemma_output(genofile_name): marker_obs.append(marker) included_markers.append(line.split("\t")[1]) - p_values.append(float(line.split("\t")[10])) + p_values.append(float(line.split("\t")[11])) return marker_obs def parse_loco_output(this_dataset, gwa_output_filename): output_filelist = [] - jsonfn = "{}/gn2/".format(TEMPDIR) + gwa_output_filename + ".json" - assert_file(jsonfn) - try: - with open(jsonfn) as data_file: - data = json.load(data_file) - except: - logger.error("Can not parse "+jsonfn) + with open("{}/gn2/".format(TEMPDIR) + gwa_output_filename + ".json") as data_file: + data = json.load(data_file) files = data['files'] for file in files: @@ -253,4 +247,4 @@ def parse_loco_output(this_dataset, gwa_output_filename): included_markers.append(line.split("\t")[1]) p_values.append(float(line.split("\t")[10])) - return marker_obs + return marker_obs \ No newline at end of file diff --git a/wqflask/wqflask/static/dbdoc/TODO.md b/wqflask/wqflask/static/dbdoc/TODO.md new file mode 100644 index 00000000..c0a8bab7 --- /dev/null +++ b/wqflask/wqflask/static/dbdoc/TODO.md @@ -0,0 +1 @@ +TODO: Add all database documentation into this folder diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html index fa9e3585..1254ea6a 100644 --- a/wqflask/wqflask/templates/correlation_page.html +++ b/wqflask/wqflask/templates/correlation_page.html @@ -1,9 +1,10 @@ {% extends "base.html" %} {% block css %} + <link rel="stylesheet" type="text/css" href="/static/new/packages/tabulator/css/tabulator.css" /> + <!-- <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" /> - <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" /> - <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" /> <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.bootstrap.css" /> + --> {% endblock %} {% block content %} @@ -63,15 +64,16 @@ </div> <div style="width: {% if target_dataset.type == "ProbeSet" %}1600px{% elif target_dataset.type == "Publish" %}1400px{% else %}800px{% endif %};"> - <table id="trait_table" class="display dataTable nowrap" style="float: left;"> + <table id="trait_table" class="display dataTable nowrap" style="font-size: 12px; float: left;"> +<!-- <thead> <tr> - <th style="width: 30px;"></th> + <th></th> {% for header in target_dataset.header_fields %} {% if header == 'Year' %} <th>{{header}}</th> {% elif header == 'Max LRS' %} - <th>Max LRS<a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup style="color:#f00"> ?</sup></a></th> + <th>Max LRS</th> {% elif header == 'Max LRS Location' %} <th>{{header}}</th> {% elif header == 'Location' %} @@ -79,7 +81,7 @@ {% elif header == 'Mean' %} <th>{{header}}</th> {% elif header == 'Additive Effect' %} - <th>Additive Effect<a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="color:#f00"> ?</sup></a></th> + <th>Additive Effect</th> {% elif header == 'Index' %} <th>{{header}}</th> {% elif header == 'N' %} @@ -91,7 +93,7 @@ {% if target_dataset.type == "ProbeSet" %} {% if corr_method == 'pearson' %} <th>Sample r</th> - <th> N</th> + <th>N</th> <th>Sample p(r)</th> <th>Lit r</th> <th>Tissue r</th> @@ -129,8 +131,8 @@ <tbody> {% for trait in correlation_results %} <tr> - <td style="padding-left: 8px; padding-right: 0px; padding-top: 4px; align: center;"><INPUT TYPE="checkbox" NAME="searchResult" class="checkbox trait_checkbox" style="padding-right: 0px;" VALUE="{{ data_hmac('{}:{}'.format(trait.name, trait.dataset.name)) }}"></td> - <td align="right">{{ loop.index }}</td> + <td><INPUT TYPE="checkbox" NAME="searchResult" class="checkbox trait_checkbox" style="padding-right: 0px;" VALUE="{{ data_hmac('{}:{}'.format(trait.name, trait.dataset.name)) }}"></td> + <td style="padding-left: 8px; padding-right: 0px; padding-top: 4px; align: center; display: inline;">{{ loop.index }}</td> <td> <a href="{{ url_for('show_trait_page', trait_id = trait.name, @@ -183,6 +185,7 @@ </tr> {% endfor %} </tbody> +--> </table> </div> </div> @@ -191,13 +194,17 @@ {% block js %} <script type="text/javascript" src="/static/new/javascript/search_results.js"></script> + <script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script> + <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script> + <script language="javascript" type="text/javascript" src="/static/new/packages/tabulator/js/tabulator.js"></script> + <!-- <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.js"></script> <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/dataTables.buttons.min.js"></script> <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/buttons.html5.min.js"></script> <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/buttons.bootstrap.min.js"></script> - <script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script> <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script> - <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script> + --> + <script type="text/javascript" charset="utf-8"> function getValue(x) { if (x.indexOf('input') >= 0) { @@ -213,7 +220,8 @@ } return parseFloat(x); } - + +/* jQuery.fn.dataTableExt.oSort['numeric-html-asc'] = function(a,b) { a = Math.abs(parseFloat($(a).text())); b = Math.abs(parseFloat($(b).text())); @@ -259,10 +267,60 @@ var y = parseFloat(b); return ((x < y) ? 1 : ((x > y) ? -1 : 0)); }; - +*/ $(document).ready( function () { + var table_json = {{ json_results | safe }} + + + {% if target_dataset.type == "ProbeSet" %} + var json_array = new Array(); + + for (i=0; i < table_json.length; i++){ + json_array.push({ + checkbox: table_json[i]["checkbox"], + index: table_json[i]["index"], + trait_id: table_json[i]["trait_id"], + symbol: table_json[i]["symbol"], + description: table_json[i]["description"], + location: table_json[i]["location"], + mean: table_json[i]["mean"], + lrs_score: table_json[i]["lrs_score"], + lrs_location: table_json[i]["lrs_location"], + additive: table_json[i]["additive"], + sample_r: table_json[i]["sample_r"], + num_overlap: table_json[i]["num_overlap"], + sample_p: table_json[i]["sample_p"], + lit_corr: table_json[i]["lit_corr"], + tissue_corr: table_json[i]["tissue_corr"] + }); + console.log("JSON_DATA:", json_array); + } + //console.log("JSON_DATA:", json_array) + + $("#trait_table").tabulator({ + data: json_array, + columns:[ + {title:"", field:"checkbox", formatter:"html"}, + {title:"Index", field:"index", formatter:"plaintext"}, + {title:"Record", field:"trait_id", formatter:"html"}, + {title:"Symbol", field:"symbol", formatter:"plaintext"}, + {title:"Description", field:"description", formatter:"textarea", width:"25%"}, + {title:"Location", field:"location", formatter:"plaintext"}, + {title:"Mean", field:"mean", formatter:"plaintext"}, + {title:"Max LRS", field:"lrs_score", formatter:"plaintext"}, + {title:"Max LRS Location", field:"lrs_location", formatter:"plaintext"}, + {title:"Additive Effect", field:"additive", formatter:"plaintext"}, + {title:"Sample r", field:"sample_r", formatter:"html"}, + {title:"N", field:"num_overlap", formatter:"plaintext"}, + {title:"Sample p(r)", field:"sample_p", formatter:"plaintext"}, + {title:"Lit r", field:"lit_corr", formatter:"plaintext"}, + {title:"Tissue r", field:"tissue_corr", formatter:"plaintext"} + ] + }); + {% endif %} + $('#trait_table tr').click(function(event) { if (event.target.type !== 'checkbox') { $(':checkbox', this).trigger('click'); @@ -296,6 +354,7 @@ } } + /* console.time("Creating table"); {% if target_dataset.type == "ProbeSet" %} @@ -447,6 +506,7 @@ } ); {% endif %} console.timeEnd("Creating table"); + */ submit_special = function(url) { $("#correlation_form").attr("action", url); diff --git a/wqflask/wqflask/templates/empty_collection.html b/wqflask/wqflask/templates/empty_collection.html new file mode 100644 index 00000000..d1b779ef --- /dev/null +++ b/wqflask/wqflask/templates/empty_collection.html @@ -0,0 +1,15 @@ +{% extends "base.html" %} +{% block title %}{{ tool }}{% endblock %} +{% block content %} +<!-- Start of body --> + {{ header("Error") }} + + <div class="container"> + <input type="hidden" name="uc_id" id="uc_id" value="{{ uc_id }}"> + <p>You must select at least two traits to use the {{ tool }}.</p> + </div> + + +<!-- End of body --> + +{% endblock %} diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 4e81c29c..187b60dc 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -743,7 +743,7 @@ def corr_matrix_page(): start_vars = request.form traits = [trait.strip() for trait in start_vars['trait_list'].split(',')] - if traits[0] != "": + if len(traits) > 1: template_vars = show_corr_matrix.CorrelationMatrix(start_vars) template_vars.js_data = json.dumps(template_vars.js_data, default=json_default_handler, |