diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/correlation/correlation_gn3_api.py | 127 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/test_correlation_page.html | 8 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/tutorials.html | 1 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 4 |
4 files changed, 95 insertions, 45 deletions
diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py index 98d52591..46202ca3 100644 --- a/wqflask/wqflask/correlation/correlation_gn3_api.py +++ b/wqflask/wqflask/correlation/correlation_gn3_api.py @@ -41,27 +41,33 @@ def process_samples(start_vars, sample_names, excluded_samples=None): return sample_data +def merge_correlation_results(correlation_results, target_correlation_results): + + corr_dict = {} + + for trait_dict in target_correlation_results: + for trait_name, values in trait_dict.items(): + + corr_dict[trait_name] = values + for trait_dict in correlation_results: + for trait_name, values in trait_dict.items(): + + if corr_dict.get(trait_name): + + trait_dict[trait_name].update(corr_dict.get(trait_name)) + + return correlation_results + + def sample_for_trait_lists(corr_results, target_dataset, this_trait, this_dataset, start_vars): """interface function for correlation on top results""" - sample_data = process_samples( - start_vars, this_dataset.group.samplelist) - target_dataset.get_trait_data(list(sample_data.keys())) - # should filter target traits from here - _corr_results = corr_results - - this_trait = retrieve_sample_data(this_trait, this_dataset) - - this_trait_data = { - "trait_sample_data": sample_data, - "trait_id": start_vars["trait_id"] - } - results = map_shared_keys_to_values( - target_dataset.samplelist, target_dataset.trait_data) + (this_trait_data, target_dataset) = fetch_sample_data( + start_vars, this_trait, this_dataset, target_dataset) correlation_results = compute_all_sample_correlation(corr_method="pearson", this_trait=this_trait_data, - target_dataset=results) + target_dataset=target_dataset) return correlation_results @@ -105,6 +111,23 @@ def lit_for_trait_list(corr_results, this_dataset, this_trait): return correlation_results +def fetch_sample_data(start_vars, this_trait, this_dataset, target_dataset): + + sample_data = process_samples( + start_vars, this_dataset.group.samplelist) + target_dataset.get_trait_data(list(sample_data.keys())) + this_trait = retrieve_sample_data(this_trait, this_dataset) + this_trait_data = { + "trait_sample_data": sample_data, + "trait_id": start_vars["trait_id"] + } + + results = map_shared_keys_to_values( + target_dataset.samplelist, target_dataset.trait_data) + + return (this_trait_data, results) + + def compute_correlation(start_vars, method="pearson"): """compute correlation for to call gn3 api""" # pylint: disable-msg=too-many-locals @@ -114,36 +137,19 @@ def compute_correlation(start_vars, method="pearson"): (this_dataset, this_trait, target_dataset, sample_data) = create_target_this_trait(start_vars) + target_dataset_type = target_dataset.type + this_dataset_type = this_dataset.type + method = start_vars['corr_sample_method'] corr_return_results = int(start_vars.get("corr_return_results", 100)) corr_input_data = {} if corr_type == "sample": - - sample_data = process_samples( - start_vars, this_dataset.group.samplelist) - target_dataset.get_trait_data(list(sample_data.keys())) - this_trait = retrieve_sample_data(this_trait, this_dataset) - this_trait_data = { - "trait_sample_data": sample_data, - "trait_id": start_vars["trait_id"] - } - results = map_shared_keys_to_values( - target_dataset.samplelist, target_dataset.trait_data) + (this_trait_data, target_dataset_data) = fetch_sample_data( + start_vars, this_trait, this_dataset, target_dataset) correlation_results = compute_all_sample_correlation(corr_method=method, this_trait=this_trait_data, - target_dataset=results) - - # do tissue correaltion - - # code to be use later - - # tissue_result = tissue_for_trait_lists( - # correlation_results, this_dataset, this_trait) - # # lit spoils the party so slow - # lit_result = lit_for_trait_list( - # correlation_results, this_dataset, this_trait) - + target_dataset=target_dataset_data) elif corr_type == "tissue": trait_symbol_dict = this_dataset.retrieve_genes("Symbol") @@ -172,7 +178,50 @@ def compute_correlation(start_vars, method="pearson"): conn=conn, trait_lists=list(geneid_dict.items()), species=species, gene_id=this_trait_geneid) - return correlation_results[0:corr_return_results] + correlation_results = correlation_results[0:corr_return_results] + + compute_all = True # later to be passed as argument + + if (compute_all): + + correlation_results = compute_corr_for_top_results(correlation_results, + this_trait, + this_dataset, + target_dataset, + corr_type) + + correlation_data = {"correlation_results": correlation_results, + "this_trait": this_trait.name, + "target_dataset": start_vars['corr_dataset'], + "return_results": corr_return_results} + + return correlation_data + + +def compute_corr_for_top_results(correlation_results, + this_trait, + this_dataset, + target_dataset, + corr_type): + if corr_type != "tissue" and this_dataset.type == "ProbeSet" and target_dataset.type == "ProbeSet": + + tissue_result = tissue_for_trait_lists( + correlation_results, this_dataset, this_trait) + + correlation_results = merge_correlation_results( + correlation_results, tissue_result) + + if corr_type != "lit" and this_dataset.type == "ProbeSet" and target_dataset.type == "ProbeSet": + lit_result = lit_for_trait_list( + correlation_results, this_dataset, this_trait) + + correlation_results = merge_correlation_results( + correlation_results, lit_result) + + if corr_type != "sample": + pass + + return correlation_results def do_lit_correlation(this_trait, this_dataset): diff --git a/wqflask/wqflask/templates/test_correlation_page.html b/wqflask/wqflask/templates/test_correlation_page.html index 037e9735..0809b65e 100644 --- a/wqflask/wqflask/templates/test_correlation_page.html +++ b/wqflask/wqflask/templates/test_correlation_page.html @@ -42,7 +42,7 @@ {% block content %} <div class="correlation-title"> - <h3>Correlation Results for <span>Dataset_name</span> against <span><a href="">trait_name</a></span> for the top <span>all</span> Results</h3> + <h3>Correlation Results for <span>{{target_dataset}}</span> against <span><a href="">{{this_trait}}</a></span> for the top <span>{{return_results}}</span> Results</h3> </div> <div class="header-toggle-vis"> <h4 style="font-weight: bolder;padding: 5px 3px;">Toggle Columns</h4> @@ -84,7 +84,6 @@ <script language="javascript" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.1/js/all.min.js"></script> <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/scroller/js/dataTables.scroller.min.js') }}"></script> <script type="text/javascript"> - console.log("running this script") let correlationResults = {{correlation_results|safe}} // document.querySelector(".content").innerHTML =correlationResults // parse the data @@ -102,7 +101,7 @@ return new_dict; }) -console.log(correlationResults) +console.log(correlationResults) </script> @@ -138,7 +137,8 @@ console.log(correlationResults) { "targets":2, "render":(data,type,row)=>{ - let urlLink = "/show_trait?trait_id=1453207_at&dataset=HC_M2_0606_P" + // should use a dynamic dataset name + let urlLink = `/show_trait?trait_id=${data}&dataset=HC_M2_0606_P` let traitLink = `<a href=${urlLink}>${data}</a>` return traitLink }, diff --git a/wqflask/wqflask/templates/tutorials.html b/wqflask/wqflask/templates/tutorials.html index ce5d0e3d..ed1b6f3a 100644 --- a/wqflask/wqflask/templates/tutorials.html +++ b/wqflask/wqflask/templates/tutorials.html @@ -10,6 +10,7 @@ <LI><A HREF="http://www.nervenet.org/tutorials/HS_Rat_Using_GeneNetwork_21Apr2020v7.pptx">Statistical and genetic functions, and initial mapping results for Rat GWAS P50 as implemented in GeneNetwork.org</A></LI> <LI><A HREF="https://opar.io/training/osga-webinar-series-2020.html">Webinar Series - Quantitative Genetics Tools for Mapping Trait Variation to Mechanisms, Therapeutics, and Interventions</A></LI> + <LI><A HREF="https://opar.io/training/osga-webinar-series-2020.html">TESTING</A></LI> </UL> <P></P> </TD> diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 3c875163..4834ee63 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -972,8 +972,8 @@ def corr_compute_page(): @app.route("/test_corr_compute", methods=["POST"]) def test_corr_compute_page(): - correlation_results = compute_correlation(request.form) - return render_template("test_correlation_page.html", correlation_results=correlation_results) + correlation_data = compute_correlation(request.form) + return render_template("test_correlation_page.html", **correlation_data) @app.route("/corr_matrix", methods=('POST',)) def corr_matrix_page(): |