From a91c0c240e3534567f65b16578bcfaf72a9055c9 Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 12 Feb 2018 17:08:58 +0000 Subject: Quick parallel correlation should work, though I'm not sure why the code suddenly decided to start running it when it wasn't in the past. Switched correlation table to tabulator --- wqflask/wqflask/correlation/show_corr_results.py | 22 +++++++++- wqflask/wqflask/templates/correlation_page.html | 51 ++++++++++++++++++------ 2 files changed, 58 insertions(+), 15 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 24432ad0..bb109f60 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -120,8 +120,15 @@ class CorrelationResults(object): self.min_expr = float(start_vars['min_expr']) else: self.min_expr = None - self.p_range_lower = float(start_vars['p_range_lower']) - self.p_range_upper = float(start_vars['p_range_upper']) + logger.debug("P RANGE:", start_vars['p_range_lower']) + try: + self.p_range_lower = float(start_vars['p_range_lower']) + except: + self.p_range_lower = -1.00 + try: + self.p_range_upper = float(start_vars['p_range_upper']) + except: + self.p_range_upper = 1.00 if ('loc_chr' in start_vars and 'min_loc_mb' in start_vars and @@ -1153,6 +1160,17 @@ 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 = [] diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html index fa9e3585..c7fb7cc6 100644 --- a/wqflask/wqflask/templates/correlation_page.html +++ b/wqflask/wqflask/templates/correlation_page.html @@ -1,9 +1,10 @@ {% extends "base.html" %} {% block css %} + + {% endblock %} {% block content %} @@ -63,15 +64,14 @@
- +
- {% for header in target_dataset.header_fields %} {% if header == 'Year' %} {% elif header == 'Max LRS' %} - + {% elif header == 'Max LRS Location' %} {% elif header == 'Location' %} @@ -79,7 +79,7 @@ {% elif header == 'Mean' %} {% elif header == 'Additive Effect' %} - + {% elif header == 'Index' %} {% elif header == 'N' %} @@ -91,7 +91,7 @@ {% if target_dataset.type == "ProbeSet" %} {% if corr_method == 'pearson' %} - + @@ -129,8 +129,7 @@ {% for trait in correlation_results %} - - + {% for uc in collections %} + {% if g.user_session.user_ob %} + {% else %} + + {% endif %} diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html index 1254ea6a..0d305559 100644 --- a/wqflask/wqflask/templates/correlation_page.html +++ b/wqflask/wqflask/templates/correlation_page.html @@ -275,29 +275,32 @@ {% if target_dataset.type == "ProbeSet" %} - var json_array = new Array(); + var json_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); + this_array = json_array + + var row_dict = {}; + row_dict.checkbox = table_json[i]["checkbox"] + row_dict.index = table_json[i]["index"] + row_dict.trait_id = table_json[i]["trait_id"] + row_dict.symbol = table_json[i]["symbol"] + row_dict.description = table_json[i]["description"] + row_dict.location = table_json[i]["location"] + row_dict.mean = table_json[i]["mean"] + row_dict.lrs_score = table_json[i]["lrs_score"] + row_dict.lrs_location = table_json[i]["lrs_location"] + row_dict.additive = table_json[i]["additive"] + row_dict.sample_r = table_json[i]["sample_r"] + row_dict.num_overlap = table_json[i]["num_overlap"] + row_dict.sample_p = table_json[i]["sample_p"] + row_dict.lit_corr = table_json[i]["lit_corr"] + row_dict.tissue_corr = table_json[i]["tissue_corr"] + this_array.push(row_dict); + json_array.concat(this_array); + //console.log("JSON_ARRAY:", json_array); } - //console.log("JSON_DATA:", json_array) + console.log("JSON_DATA:", json_array) $("#trait_table").tabulator({ data: json_array, diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index dcec2b9e..ab2e2aae 100644 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html @@ -1,6 +1,6 @@
{% if (use_pylmm_rqtl and dataset.group.species != "human") or use_plink_gemma %} -
+
    @@ -38,11 +38,11 @@ {# if use_pylmm_rqtl and not use_plink_gemma and dataset.group.species != "human" #} {% if dataset.group.mapping_id == "1" %}
    -
    +
    {% if genofiles and genofiles|length>0 %}
    - -
    + +
    - -
    + +
    +
    - - + +
    + + {% endif %} +
    +
    +
    + +
    + +
    - +
    {% if genofiles and genofiles|length>0 %}
    - -
    + +
    - -
    + +
    - -
    + +
    {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %} {% else %} @@ -162,8 +184,8 @@
    - -
    + +
    -
    -
    - +
    + +
    +
    @@ -189,8 +212,8 @@
    {% if genofiles and genofiles|length>0 %}
    - -
    + +
    + +
    +
    -
    - -
    + +
    {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %} {% else %} @@ -228,8 +248,8 @@
    - -
    + +
    - -
    + +
    -
    -
    - +
    + +
    +
    @@ -295,8 +316,8 @@
    {% if genofiles and genofiles|length>0 %}
    - -
    + +
    {% for item in genofiles %} @@ -365,29 +354,34 @@
    {% endif %}
    - -
    + +
    -
    - -
    - - + +
    + {% if g.user_session.user_ob and (g.user_session.user_ob.display_num_collections() == "") %} + No collections available. Please add traits to a collection to use them as covariates. + {% elif g.cookie_session.display_num_collections() == "" %} + No collections available. Please add traits to a collection to use them as covariates. + {% else %} +
    + + +
    + + {% endif %} +
    -
    - -
    -
    +
    + +
    +
    @@ -416,7 +410,7 @@
    -
    +
    {% if dataset.group.mapping_id == "1" %}
    Interval Mapping
    -- cgit v1.2.3 From cbc4e864f3d05da3da54a14a3cad3ea0d18d087f Mon Sep 17 00:00:00 2001 From: zsloan Date: Thu, 15 Mar 2018 17:59:35 +0000 Subject: Changed appearance of mapping and correlation options on trait page Fixed issue where changed sample values were not passed to qtlreaper mapping ("Interval Mapping") Loading factors and their plot are hidden in situations where there's some error with calculating principal components Added GEMMA description and changed order of descriptions for mapping options on trait page --- .../wqflask/correlation_matrix/show_corr_matrix.py | 9 +- .../wqflask/marker_regression/marker_regression.py | 1 + .../marker_regression/marker_regression_gn1.py | 2 + .../wqflask/marker_regression/qtlreaper_mapping.py | 17 ++-- wqflask/wqflask/templates/correlation_matrix.html | 3 +- .../show_trait_calculate_correlations.html | 106 ++++++++++----------- .../templates/show_trait_mapping_tools.html | 98 ++++++++++--------- wqflask/wqflask/views.py | 2 +- 8 files changed, 125 insertions(+), 113 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py index b34beb7b..077386a3 100644 --- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py +++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py @@ -173,9 +173,12 @@ class CorrelationMatrix(object): for sample in self.all_sample_list: groups.append(1) - pca = self.calculate_pca(range(len(self.traits)), corr_eigen_value, corr_eigen_vectors) - - self.loadings_array = self.process_loadings() + try: + self.pca_works = "True" + pca = self.calculate_pca(range(len(self.traits)), corr_eigen_value, corr_eigen_vectors) + self.loadings_array = self.process_loadings() + except: + self.pca_works = "False" self.js_data = dict(traits = [trait.name for trait in self.traits], groups = groups, diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index 087b95b4..db4f8f46 100644 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -228,6 +228,7 @@ class MarkerRegression(object): results, self.json_data, self.perm_output, self.suggestive, self.significant, self.bootstrap_results = qtlreaper_mapping.gen_reaper_results(self.this_trait, self.dataset, self.samples, + self.vals, self.json_data, self.num_perm, self.bootCheck, diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py index 211cf187..66884b0c 100644 --- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py +++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py @@ -1204,6 +1204,8 @@ class MarkerRegression(object): else: if self.mapping_method == "gemma" or self.mapping_method == "gemma_bimbam": string2 = 'Using GEMMA mapping method with no control for other QTLs.' + if self.covariates != "": + string3 = 'Using following traits as covariates: ' + self.covariates elif self.mapping_method == "rqtl_plink" or self.mapping_method == "rqtl_geno": string2 = 'Using R/qtl mapping method with no control for other QTLs.' elif self.mapping_method == "plink": diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py index 50228b5e..6b58190f 100644 --- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py +++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py @@ -1,17 +1,20 @@ -def gen_reaper_results(this_trait, dataset, samples_before, json_data, num_perm, bootCheck, num_bootstrap, do_control, control_marker, manhattan_plot): +import utility.logger +logger = utility.logger.getLogger(__name__ ) + +def gen_reaper_results(this_trait, dataset, samples_before, trait_vals, json_data, num_perm, bootCheck, num_bootstrap, do_control, control_marker, manhattan_plot): genotype = dataset.group.read_genotype_file() if manhattan_plot != True: genotype = genotype.addinterval() - samples, values, variances, sample_aliases = this_trait.export_informative() - trimmed_samples = [] trimmed_values = [] - for i in range(0, len(samples)): - if this_trait.data[samples[i]].name in samples_before: - trimmed_samples.append(samples[i]) - trimmed_values.append(values[i]) + for i in range(0, len(samples_before)): + try: + trimmed_values.append(float(trait_vals[i])) + trimmed_samples.append(samples_before[i]) + except: + pass perm_output = [] bootstrap_results = [] diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html index ab793d58..d27788a8 100644 --- a/wqflask/wqflask/templates/correlation_matrix.html +++ b/wqflask/wqflask/templates/correlation_matrix.html @@ -61,6 +61,7 @@
    +{% if pca_works == "True" %}

    Factor Loadings Plot

    @@ -93,7 +94,7 @@
{{header}}Max LRS ?Max LRS{{header}}{{header}}Additive Effect ?Additive Effect{{header}}Sample r  NN Sample p(r) Lit r Tissue r
{{ loop.index }}{{ loop.index }} + + + + + - {% endblock %} -- cgit v1.2.3 From 04240ba98c040887a318b9f19dff0be3f68f5e4d Mon Sep 17 00:00:00 2001 From: zsloan Date: Mon, 26 Feb 2018 23:01:55 +0000 Subject: Committing some in-progress changes related to loading correlation page from JSON --- wqflask/wqflask/correlation/show_corr_results.py | 63 ++++++++++++++++++++++- wqflask/wqflask/static/dbdoc/TODO.md | 1 + wqflask/wqflask/templates/correlation_page.html | 65 ++++++++++++++++++------ wqflask/wqflask/templates/empty_collection.html | 2 +- wqflask/wqflask/views.py | 2 +- 5 files changed, 115 insertions(+), 18 deletions(-) create mode 100644 wqflask/wqflask/static/dbdoc/TODO.md (limited to 'wqflask') diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 4d7fea61..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 @@ -1431,3 +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'] = "" + results_dict['index'] = i + 1 + results_dict['trait_id'] = ""+str(trait.name)+"" + 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'] = "" + "%0.3f" % float(trait.sample_r) + "" + 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'] = " " + trait.pubmed_text + "" + 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'] = "" + "%0.3f" % trait.sample_r + "" + 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'] = "" + "%0.3f" % float(trait.sample_r) + "" + 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/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 629724c0..1254ea6a 100644 --- a/wqflask/wqflask/templates/correlation_page.html +++ b/wqflask/wqflask/templates/correlation_page.html @@ -65,8 +65,10 @@
+
@@ -267,24 +271,55 @@ $(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:"Index", formatter:"html"}, - {title:"Record", formatter:"html"}, - {title:"Symbol", formatter:"plaintext"}, - {title:"Description", formatter:"textarea", width:"25%"}, - {title:"Location", formatter:"plaintext"}, - {title:"Mean", formatter:"plaintext"}, - {title:"Max LRS", formatter:"plaintext"}, - {title:"Max LRS Location", formatter:"plaintext"}, - {title:"Additive Effect", formatter:"plaintext"}, - {title:"Sample r", formatter:"html"}, - {title:"N", formatter:"plaintext"}, - {title:"Sample p(r)", formatter:"plaintext"}, - {title:"Lit r", formatter:"plaintext"}, - {title:"Tissue r", formatter:"plaintext"} + {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') { diff --git a/wqflask/wqflask/templates/empty_collection.html b/wqflask/wqflask/templates/empty_collection.html index 3f2b3786..d1b779ef 100644 --- a/wqflask/wqflask/templates/empty_collection.html +++ b/wqflask/wqflask/templates/empty_collection.html @@ -6,7 +6,7 @@
-

You must select at least one trait to use the {{ tool }}.

+

You must select at least two traits to use the {{ tool }}.

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, -- cgit v1.2.3 From 51383c96dc275f4462716398f9ec665fbd84802a Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 2 Mar 2018 17:59:28 +0000 Subject: Added option to display selected covariates for GEMMA mapping Changed layout/appearance of mapping options Partially fixed issue with deleting collections Changes to correlation table still in progress; having trouble getting tabulator to load JSON --- wqflask/wqflask/collect.py | 7 +- wqflask/wqflask/marker_regression/gemma_mapping.py | 4 +- .../javascript/get_covariates_from_collection.js | 5 + .../wqflask/static/new/javascript/show_trait.js | 3 +- wqflask/wqflask/templates/collections/list.html | 12 +- wqflask/wqflask/templates/correlation_page.html | 43 +++-- .../templates/show_trait_mapping_tools.html | 208 ++++++++++----------- 7 files changed, 146 insertions(+), 136 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py index 2f6c3a96..0f72b29d 100644 --- a/wqflask/wqflask/collect.py +++ b/wqflask/wqflask/collect.py @@ -349,8 +349,11 @@ def delete_collection(): db_session.delete(uc) db_session.commit() else: - collection_name = params['collection_name'] - user_manager.AnonUser().delete_collection(collection_name) + if "collection_name" in params: + collection_name = params['collection_name'] + else: + for this_collection in params['uc_id'].split(":"): + user_manager.AnonUser().delete_collection(this_collection) flash("We've deleted the collection: {}.".format(collection_name), "alert-info") diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index 233a5c76..7563eb2c 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -235,7 +235,7 @@ def parse_loco_output(this_dataset, gwa_output_filename): else: marker['chr'] = line.split("\t")[0] 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 @@ -245,6 +245,6 @@ def parse_loco_output(this_dataset, gwa_output_filename): 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 \ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js b/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js index 92e2b13b..f2e694d8 100644 --- a/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js +++ b/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js @@ -24,6 +24,7 @@ collection_click = function() { submit_click = function() { var covariates_string = ""; + var covariates_display_string = ""; $('#collections_holder').find('input[type=checkbox]:checked').each(function() { var this_dataset, this_trait; this_trait = $(this).parents('tr').find('.trait').text(); @@ -31,12 +32,15 @@ submit_click = function() { this_dataset = $(this).parents('tr').find('.dataset').text(); console.log("this_dataset is:", this_dataset); covariates_string += this_trait + ":" + this_dataset + "," + covariates_display_string += this_trait + "\n" }); // Trim the last comma covariates_string = covariates_string.substring(0, covariates_string.length - 1) + //covariates_display_string = covariates_display_string.substring(0, covariates_display_string.length - 2) console.log("COVARIATES:", covariates_string) $("input[name=covariates]").val(covariates_string) + $(".selected_covariates").val(covariates_display_string) return $.colorbox.close(); }; @@ -46,6 +50,7 @@ trait_click = function() { trait = $(this).parent().find('.trait').text(); dataset = $(this).parent().find('.dataset').text(); $("input[name=covariates]").val(trait + ":" + dataset) + $(".selected_covariates").text(trait) return $.colorbox.close(); }; diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js index 099d8010..df10c060 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.js +++ b/wqflask/wqflask/static/new/javascript/show_trait.js @@ -88,7 +88,8 @@ }; })(this)); $("#remove_covariates").click(function () { - $("input[name=covariates]").val("") + $("input[name=covariates]").val("") + $(".selected_covariates").val("") }); d3.select("#clear_compare_trait").on("click", (function(_this) { return function() { diff --git a/wqflask/wqflask/templates/collections/list.html b/wqflask/wqflask/templates/collections/list.html index ad72052e..e7f3229b 100644 --- a/wqflask/wqflask/templates/collections/list.html +++ b/wqflask/wqflask/templates/collections/list.html @@ -26,13 +26,13 @@ {% endif %}
-
- -
+
+ +
- +

@@ -51,7 +51,11 @@
{{ loop.index }} {% if g.user_session.user_ob %} {{ uc.name }}
- +{% endif %} {% endblock %} {% block js %} diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html index c5f815ce..ef233333 100644 --- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html +++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html @@ -1,9 +1,10 @@
+
- -
+ +
{% for tissue in corr_tools.dataset_menu %} {% if tissue.tissue %} @@ -37,8 +38,8 @@
- -
+ +
{% for group, pretty_group in sample_group_types.items() %} @@ -64,8 +65,8 @@
- -
+ +
- -
+ +
Chr:     Mb:  to  @@ -89,8 +90,8 @@
- -
+ +
@@ -103,48 +104,45 @@
- -
+ +
- -
- -
- - The Sample Correlation - is computed - between trait data and any - other traits in the sample database selected above. Use - Spearman - Rank - when the sample size is small (<20) or when there are influential outliers. - - - -
-
+
+
+ + The Sample Correlation + is computed + between trait data and any + other traits in the sample database selected above. Use + Spearman + Rank + when the sample size is small (<20) or when there are influential outliers. + + + +
\ No newline at end of file diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index ab2e2aae..03590c2c 100644 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html @@ -1,5 +1,5 @@
- {% if (use_pylmm_rqtl and dataset.group.species != "human") or use_plink_gemma %} + {% if dataset.group.mapping_names|length > 0 %}
@@ -41,7 +41,7 @@
{% if genofiles and genofiles|length>0 %}
- +
- -
+ +
@@ -75,7 +75,7 @@
-->
- +
{% if g.user_session.user_ob and (g.user_session.user_ob.display_num_collections() == "") %} No collections available. Please add traits to a collection to use them as covariates. @@ -86,13 +86,13 @@
- + {% endif %}
- -
+ +
@@ -116,7 +116,7 @@
{% if genofiles and genofiles|length>0 %}
- +
- +
- -
+ +
{% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %} {% else %} @@ -184,8 +184,8 @@
- -
+ +
- -
+ +
@@ -212,7 +212,7 @@
{% if genofiles and genofiles|length>0 %}
- +
- -
+ +
{% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %} {% else %} @@ -248,7 +248,7 @@
- +
@@ -289,8 +289,8 @@
-->
- -
+ +
- -
+ +
@@ -316,7 +316,7 @@
{% if genofiles and genofiles|length>0 %}
- +
{% for item in genofiles %} @@ -354,13 +354,13 @@
{% endif %}
- +
- +
{% if g.user_session.user_ob and (g.user_session.user_ob.display_num_collections() == "") %} No collections available. Please add traits to a collection to use them as covariates. @@ -376,8 +376,8 @@
- -
+ +
@@ -389,16 +389,16 @@